Merge branch 'master' of github.com:gephi/gephi

modules/AppearanceAPI/src/main/java/org/gephi/appearance/AppearanceModelImpl.java

@@ -217,7 +217,7 @@ public class AppearanceModelImpl implements AppearanceModel {
         }
     }
 
-    public boolean isPartition(Column column) {
+    private boolean isPartition(Column column) {
         Index index;
         if (AttributeUtils.isNodeColumn(column)) {
             index = localScale ? graphModel.getNodeIndex(graphModel.getVisibleView()) : graphModel.getNodeIndex();
@@ -246,7 +246,7 @@ public class AppearanceModelImpl implements AppearanceModel {
         return false;
     }
 
-    public boolean isRanking(Column column) {
+    private boolean isRanking(Column column) {
         if (column.isNumber()) {
             Index index;
             if (AttributeUtils.isNodeColumn(column)) {

modules/AppearanceAPI/src/main/java/org/gephi/appearance/FunctionImpl.java

@@ -165,4 +165,38 @@ public class FunctionImpl implements RankingFunction, PartitionFunction, SimpleF
         }
         return super.toString();
     }
+
+    @Override
+    public int hashCode() {
+        int hash = 5;
+        hash = 47 * hash + (this.column != null ? this.column.hashCode() : 0);
+        hash = 47 * hash + (this.transformer != null ? this.transformer.hashCode() : 0);
+        hash = 47 * hash + (this.partition != null ? this.partition.hashCode() : 0);
+        hash = 47 * hash + (this.ranking != null ? this.ranking.hashCode() : 0);
+        return hash;
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (obj == null) {
+            return false;
+        }
+        if (getClass() != obj.getClass()) {
+            return false;
+        }
+        final FunctionImpl other = (FunctionImpl) obj;
+        if (this.column != other.column && (this.column == null || !this.column.equals(other.column))) {
+            return false;
+        }
+        if (this.transformer != other.transformer && (this.transformer == null || !this.transformer.equals(other.transformer))) {
+            return false;
+        }
+        if (this.partition != other.partition && (this.partition == null || !this.partition.equals(other.partition))) {
+            return false;
+        }
+        if (this.ranking != other.ranking && (this.ranking == null || !this.ranking.equals(other.ranking))) {
+            return false;
+        }
+        return true;
+    }
 }

modules/AppearanceAPI/src/main/java/org/gephi/appearance/PartitionImpl.java

@@ -104,4 +104,26 @@ public class PartitionImpl implements Partition {
     public Column getColumn() {
         return column;
     }
+
+    @Override
+    public int hashCode() {
+        int hash = 3;
+        hash = 23 * hash + (this.column != null ? this.column.hashCode() : 0);
+        return hash;
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (obj == null) {
+            return false;
+        }
+        if (getClass() != obj.getClass()) {
+            return false;
+        }
+        final PartitionImpl other = (PartitionImpl) obj;
+        if (this.column != other.column && (this.column == null || !this.column.equals(other.column))) {
+            return false;
+        }
+        return true;
+    }
 }

modules/AppearanceAPI/src/main/java/org/gephi/appearance/RankingImpl.java

@@ -69,7 +69,7 @@ public class RankingImpl implements Ranking {
 
     @Override
     public Number getMaxValue() {
-        return index.getMinValue(column);
+        return index.getMaxValue(column);
     }
 
     @Override
@@ -87,4 +87,26 @@ public class RankingImpl implements Ranking {
         float normalizedValue = (float) (value.doubleValue() - getMinValue().doubleValue()) / (float) (getMaxValue().doubleValue() - getMinValue().doubleValue());
         return interpolator.interpolate(normalizedValue);
     }
+
+    @Override
+    public int hashCode() {
+        int hash = 3;
+        hash = 67 * hash + (this.column != null ? this.column.hashCode() : 0);
+        return hash;
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (obj == null) {
+            return false;
+        }
+        if (getClass() != obj.getClass()) {
+            return false;
+        }
+        final RankingImpl other = (RankingImpl) obj;
+        if (this.column != other.column && (this.column == null || !this.column.equals(other.column))) {
+            return false;
+        }
+        return true;
+    }
 }

modules/DesktopAppearance/pom.xml

@@ -20,6 +20,10 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>project-api</artifactId>
         </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>graph-api</artifactId>
+        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>appearance-api</artifactId>

modules/DesktopAppearance/src/main/java/org/gephi/desktop/appearance/AppearanceUIController.java

@@ -49,12 +49,17 @@ import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.Map;
 import java.util.Set;
+import java.util.Timer;
+import java.util.TimerTask;
 import org.gephi.appearance.api.AppearanceController;
 import org.gephi.appearance.api.AppearanceModel;
 import org.gephi.appearance.api.Function;
 import org.gephi.appearance.spi.Transformer;
 import org.gephi.appearance.spi.TransformerCategory;
 import org.gephi.appearance.spi.TransformerUI;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.TableObserver;
+import org.gephi.graph.api.GraphController;
 import org.gephi.project.api.ProjectController;
 import org.gephi.project.api.Workspace;
 import org.gephi.project.api.WorkspaceListener;
@@ -79,6 +84,8 @@ public class AppearanceUIController {
     private final Set<AppearanceUIModelListener> listeners;
     //Model
     private AppearanceUIModel model;
+    //Observer
+    private ColumnObserver tableObserver;
 
     public AppearanceUIController() {
         final ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);
@@ -98,6 +105,12 @@ public class AppearanceUIController {
                     workspace.add(model);
                 }
                 model.select();
+                if (tableObserver != null) {
+                    tableObserver.destroy();
+                }
+                tableObserver = new ColumnObserver(workspace);
+                tableObserver.start();
+
                 firePropertyChangeEvent(AppearanceUIModelEvent.MODEL, oldModel, model);
             }
 
@@ -117,6 +130,9 @@ public class AppearanceUIController {
                 AppearanceUIModel oldModel = model;
                 model = null;
                 firePropertyChangeEvent(AppearanceUIModelEvent.MODEL, oldModel, model);
+                if (tableObserver != null) {
+                    tableObserver.destroy();
+                }
             }
         });
 
@@ -260,4 +276,43 @@ public class AppearanceUIController {
             listener.propertyChange(event);
         }
     }
+
+    private class ColumnObserver extends TimerTask {
+
+        private final GraphController gc = Lookup.getDefault().lookup(GraphController.class);
+        private static final int INTERVAL = 500;
+        private final Timer timer;
+        private final TableObserver nodeObserver;
+        private final TableObserver edgeObserver;
+
+        public ColumnObserver(Workspace workspace) {
+            timer = new Timer("RankingColumnObserver", true);
+            nodeObserver = gc.getAttributeModel(workspace).getNodeTable().getTableObserver();
+            edgeObserver = gc.getAttributeModel(workspace).getEdgeTable().getTableObserver();
+        }
+
+        @Override
+        public void run() {
+            if (nodeObserver.hasTableChanged() || edgeObserver.hasTableChanged()) {
+                Function oldValue = model.getSelectedFunction();
+                model.refreshSelectedFunction();
+                Function newValue = model.getSelectedFunction();
+                firePropertyChangeEvent(AppearanceUIModelEvent.SELECTED_FUNCTION, oldValue, newValue);
+            }
+        }
+
+        public void start() {
+            timer.schedule(this, INTERVAL, INTERVAL);
+        }
+
+        public void stop() {
+            timer.cancel();
+        }
+
+        public void destroy() {
+            stop();
+            nodeObserver.destroy();
+            edgeObserver.destroy();
+        }
+    }
 }

modules/DesktopAppearance/src/main/java/org/gephi/desktop/appearance/AppearanceUIModel.java

@@ -123,6 +123,18 @@ public class AppearanceUIModel {
         }
     }
 
+    public boolean refreshSelectedFunction() {
+        Function sFunction = getSelectedFunction();
+        if (sFunction != null && sFunction.isAttribute()) {
+            for (Function func : getSelectedElementClass().equals(AppearanceUIController.NODE_ELEMENT) ? appearanceModel.getNodeFunctions() : appearanceModel.getEdgeFunctions()) {
+                if(func.equals(sFunction)) {
+                    return false;
+                }
+            }
+        }
+        return true;
+    }
+
     public void select() {
     }
 

modules/DesktopStatistics/pom.xml

@@ -5,7 +5,7 @@
         <artifactId>gephi-parent</artifactId>
         <groupId>org.gephi</groupId>
         <version>0.9-SNAPSHOT</version>
-		<relativePath>../..</relativePath>
+        <relativePath>../..</relativePath>
     </parent>
 
     <groupId>org.gephi</groupId>
@@ -18,7 +18,7 @@
     <dependencies>
         <dependency>
             <groupId>${project.groupId}</groupId>
-            <artifactId>data-attributes-api</artifactId>
+            <artifactId>graph-api</artifactId>
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>

modules/DesktopStatistics/src/main/java/org/gephi/desktop/statistics/DynamicSettingsPanel.form

@@ -1,4 +1,4 @@
-<?xml version="1.1" encoding="UTF-8" ?>
+<?xml version="1.0" encoding="UTF-8" ?>
 
 <Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
   <AuxValues>

modules/DesktopStatistics/src/main/java/org/gephi/desktop/statistics/DynamicSettingsPanel.java

@@ -50,11 +50,14 @@ import java.util.concurrent.TimeUnit;
 import javax.swing.ComboBoxModel;
 import javax.swing.DefaultComboBoxModel;
 import javax.swing.JPanel;
-import org.gephi.data.attributes.type.Interval;
-import org.gephi.data.attributes.type.TimeInterval;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.TimeFormat;
+import org.gephi.attribute.time.Interval;
 import org.gephi.dynamic.DynamicUtilities;
 import org.gephi.dynamic.api.DynamicController;
 import org.gephi.dynamic.api.DynamicModel;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.GraphModel;
 import org.gephi.lib.validation.PositiveNumberValidator;
 import org.gephi.statistics.spi.DynamicStatistics;
 import org.gephi.ui.components.richtooltip.RichTooltip;
@@ -76,6 +79,7 @@ public class DynamicSettingsPanel extends javax.swing.JPanel {
 
     private TimeUnit windowTimeUnit = TimeUnit.DAYS;
     private TimeUnit tickTimeUnit = TimeUnit.DAYS;
+    private Interval bounds = null;
 
     public DynamicSettingsPanel() {
         initComponents();
@@ -107,42 +111,29 @@ public class DynamicSettingsPanel extends javax.swing.JPanel {
             }
         });
     }
-    Interval bounds = null;
-
+    
     public void setup(DynamicStatistics dynamicStatistics) {
-        DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
-        DynamicModel model = dynamicController.getModel();
-        TimeInterval visibleInterval = model.getVisibleInterval();
+        GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
+        GraphModel graphModel = graphController.getGraphModel();
+        AttributeModel attributeModel = graphController.getAttributeModel();
+        TimeFormat timeFormat = attributeModel.getTimeFormat();
 
         //Bounds
         bounds = dynamicStatistics.getBounds();
         if (bounds == null) {
-            double low = visibleInterval.getLow();
-            if (Double.isInfinite(low)) {
-                low = model.getMin();
-            }
-            double high = visibleInterval.getHigh();
-            if (Double.isInfinite(high)) {
-                high = model.getMax();
-            }
-            bounds = new Interval(low, high);
-        }
-        String boundsStr = "";
-        if (model.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) {
-            boundsStr = bounds.getLow() + " - " + bounds.getHigh();
-        } else {
-            boundsStr = DynamicUtilities.getXMLDateStringFromDouble(bounds.getLow()) + " - " + DynamicUtilities.getXMLDateStringFromDouble(bounds.getHigh());
+            bounds = graphModel.getTimeBoundsVisible();
         }
+        String boundsStr = timeFormat.print(bounds.getLow())+" - "+timeFormat.print(bounds.getHigh());
         currentIntervalLabel.setText(boundsStr);
 
         //TimeUnit
-        if (model.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) {
+        if (timeFormat.equals(TimeFormat.DOUBLE)) {
             windowTimeUnitCombo.setVisible(false);
             tickTimeUnitCombo.setVisible(false);
         }
 
         //Set latest selected item
-        if (!model.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) {
+        if (!timeFormat.equals(TimeFormat.DOUBLE)) {
             loadDefaultTimeUnits();
         }
 
@@ -151,7 +142,7 @@ public class DynamicSettingsPanel extends javax.swing.JPanel {
         if(bounds.getHigh() - bounds.getLow() > 1) {
             initValue = 1.;
         }
-        if (model.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) {
+        if (timeFormat.equals(TimeFormat.DOUBLE)) {
             windowTextField.setText(initValue + "");
             tickTextField.setText(initValue + "");
         } else {
@@ -162,6 +153,7 @@ public class DynamicSettingsPanel extends javax.swing.JPanel {
         //Add listeners
         windowTimeUnitCombo.addItemListener(new ItemListener() {
 
+            @Override
             public void itemStateChanged(ItemEvent e) {
                 if (e.getItem() != windowTimeUnitCombo.getSelectedItem()) {
                     refreshWindowTimeUnit();
@@ -171,6 +163,7 @@ public class DynamicSettingsPanel extends javax.swing.JPanel {
 
         tickTimeUnitCombo.addItemListener(new ItemListener() {
 
+            @Override
             public void itemStateChanged(ItemEvent e) {
                 if (e.getItem() != tickTimeUnitCombo.getSelectedItem()) {
                     refreshTickTimeUnit();

modules/DesktopStatistics/src/main/java/org/gephi/desktop/statistics/StatisticsControllerUIImpl.java

@@ -43,9 +43,6 @@ package org.gephi.desktop.statistics;
 
 import java.util.ArrayList;
 import org.gephi.desktop.statistics.api.StatisticsControllerUI;
-import org.gephi.dynamic.api.DynamicController;
-import org.gephi.dynamic.api.DynamicModelEvent;
-import org.gephi.dynamic.api.DynamicModelListener;
 import org.gephi.statistics.api.StatisticsController;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.statistics.spi.StatisticsUI;
@@ -61,23 +58,23 @@ import org.openide.util.lookup.ServiceProvider;
 @ServiceProvider(service = StatisticsControllerUI.class)
 public class StatisticsControllerUIImpl implements StatisticsControllerUI {
 
-    private final DynamicModelListener dynamicModelListener;
+//    private final DynamicModelListener dynamicModelListener;
     private StatisticsModelUIImpl model;
 
     public StatisticsControllerUIImpl() {
-        dynamicModelListener = new DynamicModelListener() {
-
-            public void dynamicModelChanged(DynamicModelEvent event) {
-                if (event.getEventType().equals(DynamicModelEvent.EventType.IS_DYNAMIC_GRAPH)) {
-                    boolean isDynamic = (Boolean) event.getData();
-                    for (StatisticsUI ui : Lookup.getDefault().lookupAll(StatisticsUI.class)) {
-                        if (ui.getCategory().equals(StatisticsUI.CATEGORY_DYNAMIC)) {
-                            setStatisticsUIVisible(ui, isDynamic);
-                        }
-                    }
-                }
-            }
-        };
+//        dynamicModelListener = new DynamicModelListener() {
+//
+//            public void dynamicModelChanged(DynamicModelEvent event) {
+//                if (event.getEventType().equals(DynamicModelEvent.EventType.IS_DYNAMIC_GRAPH)) {
+//                    boolean isDynamic = (Boolean) event.getData();
+//                    for (StatisticsUI ui : Lookup.getDefault().lookupAll(StatisticsUI.class)) {
+//                        if (ui.getCategory().equals(StatisticsUI.CATEGORY_DYNAMIC)) {
+//                            setStatisticsUIVisible(ui, isDynamic);
+//                        }
+//                    }
+//                }
+//            }
+//        };
     }
 
     public void setup(StatisticsModelUIImpl model) {
@@ -88,25 +85,25 @@ public class StatisticsControllerUIImpl implements StatisticsControllerUI {
         unsetup();
 
         if (model != null) {
-            DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
-            boolean isDynamic = dynamicController.getModel(model.getWorkspace()).isDynamicGraph();
-            if (!isDynamic) {
-                for (StatisticsUI ui : Lookup.getDefault().lookupAll(StatisticsUI.class)) {
-                    if (ui.getCategory().equals(StatisticsUI.CATEGORY_DYNAMIC)) {
-                        setStatisticsUIVisible(ui, false);
-                    }
-                }
-            }
-            //Add listener
-
-            dynamicController.addModelListener(dynamicModelListener);
+//            DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
+//            boolean isDynamic = dynamicController.getModel(model.getWorkspace()).isDynamicGraph();
+//            if (!isDynamic) {
+//                for (StatisticsUI ui : Lookup.getDefault().lookupAll(StatisticsUI.class)) {
+//                    if (ui.getCategory().equals(StatisticsUI.CATEGORY_DYNAMIC)) {
+//                        setStatisticsUIVisible(ui, false);
+//                    }
+//                }
+//            }
+//            //Add listener
+//
+//            dynamicController.addModelListener(dynamicModelListener);
         }
     }
 
     public void unsetup() {
         if (model != null) {
-            DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
-            dynamicController.removeModelListener(dynamicModelListener);
+//            DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
+//            dynamicController.removeModelListener(dynamicModelListener);
         }
     }
 

modules/DesktopStatistics/src/main/java/org/gephi/desktop/statistics/StatisticsTopComponent.java

@@ -69,15 +69,15 @@ import org.openide.windows.TopComponent;
  * @author Patick J. McSweeney
  */
 @ConvertAsProperties(dtd = "-//org.gephi.desktop.statistics//Statistics//EN",
-autostore = false)
+        autostore = false)
 @TopComponent.Description(preferredID = "StatisticsTopComponent",
-iconBase = "org/gephi/desktop/statistics/resources/small.png",
-persistenceType = TopComponent.PERSISTENCE_ALWAYS)
+        iconBase = "org/gephi/desktop/statistics/resources/small.png",
+        persistenceType = TopComponent.PERSISTENCE_ALWAYS)
 @TopComponent.Registration(mode = "filtersmode", openAtStartup = true, roles = {"overview"})
 @ActionID(category = "Window", id = "org.gephi.desktop.statistics.StatisticsTopComponent")
 @ActionReference(path = "Menu/Window", position = 1200)
 @TopComponent.OpenActionRegistration(displayName = "#CTL_StatisticsTopComponent",
-preferredID = "StatisticsTopComponent")
+        preferredID = "StatisticsTopComponent")
 public final class StatisticsTopComponent extends TopComponent implements ChangeListener {
 
     //Model

modules/ImportAPI/src/main/java/org/gephi/io/importer/api/ContainerLoader.java

@@ -41,6 +41,8 @@
  */
 package org.gephi.io.importer.api;
 
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.TimeFormat;
 import org.gephi.io.importer.spi.Importer;
 
 /**

modules/ImportAPI/src/main/java/org/gephi/io/importer/api/ContainerUnloader.java

@@ -41,6 +41,7 @@
  */
 package org.gephi.io.importer.api;
 
+import org.gephi.attribute.api.TimeFormat;
 import org.gephi.io.processor.spi.Processor;
 
 /**

modules/ImportAPI/src/main/java/org/gephi/io/importer/api/TimeFormat.java

@@ -1,10 +0,0 @@
-package org.gephi.io.importer.api;
-
-/**
- *
- * @author mbastian
- */
-public enum TimeFormat {
-
-    DATE, DATETIME, DOUBLE, TIMESTAMP
-}

modules/ImportAPI/src/main/java/org/gephi/io/importer/impl/ImportContainerImpl.java

@@ -56,6 +56,7 @@ import java.util.Collections;
 import java.util.Comparator;
 import java.util.Iterator;
 import java.util.List;
+import org.gephi.attribute.api.TimeFormat;
 import org.gephi.io.importer.api.ColumnDraft;
 import org.gephi.io.importer.api.Container;
 import org.gephi.io.importer.api.ContainerLoader;
@@ -69,7 +70,6 @@ import org.gephi.io.importer.api.Issue;
 import org.gephi.io.importer.api.Issue.Level;
 import org.gephi.io.importer.api.NodeDraft;
 import org.gephi.io.importer.api.Report;
-import org.gephi.io.importer.api.TimeFormat;
 import org.openide.util.NbBundle;
 
 /**
@@ -620,15 +620,13 @@ public class ImportContainerImpl implements Container, ContainerLoader, Containe
 
         //Clean autoNode
         if (!allowAutoNode()) {
-            for (Iterator<NodeDraftImpl> itr = nodeList.iterator(); itr.hasNext();) {
-                NodeDraftImpl node = itr.next();
+            for (NodeDraftImpl node : nodeList) {
                 if (node != null && node.isCreatedAuto()) {
                     int index = nodeMap.removeInt(node.getId());
                     nodeList.set(index, null);
                 }
             }
-            for (Iterator<EdgeDraftImpl> itr = edgeList.iterator(); itr.hasNext();) {
-                EdgeDraftImpl edge = itr.next();
+            for (EdgeDraftImpl edge : edgeList) {
                 if (edge != null && (edge.getSource().isCreatedAuto() || edge.getTarget().isCreatedAuto())) {
                     int index = edgeMap.remove(edge.getId());
                     edgeList.set(index, null);
@@ -718,7 +716,7 @@ public class ImportContainerImpl implements Container, ContainerLoader, Containe
         } else if (mergeStrategy.equals(EdgeWeightMergeStrategy.MAX)) {
             result = Math.max(source.getWeight(), dest.getWeight());
         } else if (mergeStrategy.equals(EdgeWeightMergeStrategy.MIN)) {
-            result = Math.min(source.getWeight(), dest.getWeight());;
+            result = Math.min(source.getWeight(), dest.getWeight());
         } else if (mergeStrategy.equals(EdgeWeightMergeStrategy.SUM)) {
             result = source.getWeight() + dest.getWeight();
         }

modules/ImportPlugin/src/main/java/org/gephi/io/importer/plugin/database/ImporterEdgeList.java

@@ -50,6 +50,7 @@ import java.sql.Statement;
 import java.sql.Time;
 import java.sql.Timestamp;
 import java.sql.Types;
+import org.gephi.attribute.api.TimeFormat;
 import org.gephi.io.database.drivers.SQLUtils;
 import org.gephi.io.importer.api.ColumnDraft;
 import org.gephi.io.importer.api.ContainerLoader;
@@ -63,7 +64,6 @@ import org.gephi.io.importer.api.PropertiesAssociations;
 import org.gephi.io.importer.api.PropertiesAssociations.EdgeProperties;
 import org.gephi.io.importer.api.PropertiesAssociations.NodeProperties;
 import org.gephi.io.importer.api.Report;
-import org.gephi.io.importer.api.TimeFormat;
 import org.gephi.io.importer.spi.DatabaseImporter;
 
 /**

modules/ImportPlugin/src/main/java/org/gephi/io/importer/plugin/file/ImporterGEXF.java

@@ -47,6 +47,7 @@ import java.math.BigDecimal;
 import java.math.BigInteger;
 import javax.xml.stream.*;
 import javax.xml.stream.events.XMLEvent;
+import org.gephi.attribute.api.TimeFormat;
 import org.gephi.io.importer.api.*;
 import org.gephi.io.importer.spi.FileImporter;
 import org.gephi.utils.longtask.spi.LongTask;
@@ -232,7 +233,7 @@ public class ImporterGEXF implements FileImporter, LongTask {
             } else if ("datetime".equalsIgnoreCase(timeFormat)) {
                 container.setTimeFormat(TimeFormat.DATETIME);
             } else if ("timestamp".equalsIgnoreCase(timeFormat)) {
-                container.setTimeFormat(TimeFormat.TIMESTAMP);
+                container.setTimeFormat(TimeFormat.DATETIME);
             }
         } else if (mode.equalsIgnoreCase("dynamic")) {
             container.setTimeFormat(TimeFormat.DOUBLE);

modules/StatisticsAPI/pom.xml

@@ -16,10 +16,6 @@
     <name>StatisticsAPI</name>
 
     <dependencies>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>data-attributes-api</artifactId>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>dynamic-api</artifactId>

modules/StatisticsAPI/src/main/java/org/gephi/statistics/StatisticsControllerImpl.java

@@ -42,20 +42,18 @@ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics;
 
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.TimestampIndex;
+import org.gephi.attribute.time.Interval;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Graph;
 import org.gephi.statistics.spi.StatisticsBuilder;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.statistics.api.*;
-import org.gephi.data.attributes.api.AttributeController;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.type.Interval;
-import org.gephi.data.attributes.type.TimeInterval;
-import org.gephi.dynamic.api.DynamicController;
-import org.gephi.dynamic.api.DynamicGraph;
-import org.gephi.dynamic.api.DynamicModel;
-import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphController;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalGraph;
+import org.gephi.graph.api.GraphView;
+import org.gephi.graph.api.Node;
 import org.gephi.project.api.ProjectController;
 import org.gephi.utils.longtask.spi.LongTask;
 import org.gephi.utils.longtask.api.LongTaskExecutor;
@@ -86,10 +84,12 @@ public class StatisticsControllerImpl implements StatisticsController {
         ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);
         pc.addWorkspaceListener(new WorkspaceListener() {
 
+            @Override
             public void initialize(Workspace workspace) {
                 workspace.add(new StatisticsModelImpl());
             }
 
+            @Override
             public void select(Workspace workspace) {
                 model = workspace.getLookup().lookup(StatisticsModelImpl.class);
                 if (model == null) {
@@ -98,12 +98,15 @@ public class StatisticsControllerImpl implements StatisticsController {
                 }
             }
 
+            @Override
             public void unselect(Workspace workspace) {
             }
 
+            @Override
             public void close(Workspace workspace) {
             }
 
+            @Override
             public void disable() {
                 model = null;
             }
@@ -118,6 +121,7 @@ public class StatisticsControllerImpl implements StatisticsController {
         }
     }
 
+    @Override
     public void execute(final Statistics statistics, LongTaskListener listener) {
         StatisticsBuilder builder = getBuilder(statistics.getClass());
         LongTaskExecutor executor = new LongTaskExecutor(true, "Statistics " + builder.getName(), 10);
@@ -129,6 +133,7 @@ public class StatisticsControllerImpl implements StatisticsController {
             final DynamicLongTask dynamicLongTask = new DynamicLongTask((DynamicStatistics) statistics);
             executor.execute(dynamicLongTask, new Runnable() {
 
+                @Override
                 public void run() {
                     executeDynamic((DynamicStatistics) statistics, dynamicLongTask);
                 }
@@ -137,6 +142,7 @@ public class StatisticsControllerImpl implements StatisticsController {
             LongTask task = statistics instanceof LongTask ? (LongTask) statistics : null;
             executor.execute(task, new Runnable() {
 
+                @Override
                 public void run() {
                     execute(statistics);
                 }
@@ -144,13 +150,14 @@ public class StatisticsControllerImpl implements StatisticsController {
         }
     }
 
+    @Override
     public void execute(Statistics statistics) {
         if (statistics instanceof DynamicStatistics) {
             executeDynamic((DynamicStatistics) statistics, null);
         } else {
             GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-            GraphModel graphModel = graphController.getModel();
-            AttributeModel attributeModel = Lookup.getDefault().lookup(AttributeController.class).getModel();
+            GraphModel graphModel = graphController.getGraphModel();
+            AttributeModel attributeModel = graphController.getAttributeModel();
             statistics.execute(graphModel, attributeModel);
             model.addReport(statistics);
         }
@@ -158,42 +165,23 @@ public class StatisticsControllerImpl implements StatisticsController {
 
     private void executeDynamic(DynamicStatistics statistics, DynamicLongTask dynamicLongTask) {
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        GraphModel graphModel = graphController.getModel();
-        AttributeController attributeController = Lookup.getDefault().lookup(AttributeController.class);
-        DynamicController dynamicController = Lookup.getDefault().lookup(DynamicController.class);
-        DynamicModel dynamicModel = dynamicController.getModel();
-        AttributeModel attributeModel = attributeController.getModel();
-        if (!dynamicModel.isDynamicGraph()) {
-            throw new IllegalArgumentException("The current graph must be a dynamic graph");
-        }
+        GraphModel graphModel = graphController.getGraphModel();
+        AttributeModel attributeModel = graphController.getAttributeModel();
 
         double window = statistics.getWindow();
         double tick = statistics.getTick();
         Interval bounds = statistics.getBounds();
         if (bounds == null) {
-            TimeInterval visibleInterval = dynamicModel.getVisibleInterval();
-            double low = visibleInterval.getLow();
-            if (Double.isInfinite(low)) {
-                low = dynamicModel.getMin();
-            }
-            double high = visibleInterval.getHigh();
-            if (Double.isInfinite(high)) {
-                high = dynamicModel.getMax();
-            }
-            bounds = new Interval(low, high);
+            bounds = graphModel.getTimeBoundsVisible();
             statistics.setBounds(bounds);
         }
 
-
         if (dynamicLongTask != null) {
             //Count
             int c = (int) ((bounds.getHigh() - window - bounds.getLow()) / tick);
             dynamicLongTask.start(c);
         }
 
-        HierarchicalGraph graph = graphModel.getHierarchicalGraphVisible();
-        DynamicGraph dynamicGraph = dynamicModel.createDynamicGraph(graph, bounds);
-
         //Init
         statistics.execute(graphModel, attributeModel);
 
@@ -201,7 +189,24 @@ public class StatisticsControllerImpl implements StatisticsController {
         for (double low = bounds.getLow(); low <= bounds.getHigh() - window; low += tick) {
             double high = low + window;
 
-            Graph g = dynamicGraph.getSnapshotGraph(low, high);
+//            Graph g = dynamicGraph.getSnapshotGraph(low, high);
+            
+            
+            GraphView currentView = graphModel.getVisibleView();
+            Graph graph = graphModel.getGraphVisible();
+            GraphView view = graphModel.createView();
+            Graph g = graphModel.getGraph(view);
+            
+            TimestampIndex<Node> nodeIndex = graphModel.getNodeTimestampIndex(currentView);
+            for(Node node : nodeIndex.get(low, high)) {
+                g.addNode(node);
+            }
+            
+            TimestampIndex<Edge> edgeIndex = graphModel.getEdgeTimestampIndex(currentView);
+            for(Edge edge : edgeIndex.get(low, high)) {
+                g.addEdge(edge);
+            }
+            
 
             statistics.loop(g.getView(), new Interval(low, high));
 

modules/StatisticsAPI/src/main/java/org/gephi/statistics/api/StatisticsController.java

@@ -45,7 +45,6 @@ package org.gephi.statistics.api;
 import org.gephi.project.api.Workspace;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.statistics.spi.StatisticsBuilder;
-import org.gephi.statistics.spi.StatisticsUI;
 import org.gephi.utils.longtask.api.LongTaskListener;
 import org.gephi.utils.longtask.spi.LongTask;
 

modules/StatisticsAPI/src/main/java/org/gephi/statistics/spi/DynamicStatistics.java

@@ -42,8 +42,8 @@ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics.spi;
 
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.type.Interval;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.time.Interval;
 import org.gephi.graph.api.GraphModel;
 import org.gephi.graph.api.GraphView;
 

modules/StatisticsAPI/src/main/java/org/gephi/statistics/spi/Statistics.java

@@ -42,7 +42,8 @@ Portions Copyrighted 2011 Gephi Consortium.
 */
 package org.gephi.statistics.spi;
 
-import org.gephi.data.attributes.api.AttributeModel;
+
+import org.gephi.attribute.api.AttributeModel;
 import org.gephi.graph.api.GraphModel;
 
 /**

modules/StatisticsPlugin/pom.xml

@@ -16,10 +16,6 @@
     <name>StatisticsPlugin</name>
 
     <dependencies>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>data-attributes-api</artifactId>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>dynamic-api</artifactId>

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/ClusteringCoefficient.java

@@ -1,43 +1,43 @@
 /*
-Copyright 2008-2011 Gephi
-Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2011 Gephi
+ Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s):
+ Contributor(s):
 
-Portions Copyrighted 2011 Gephi Consortium.
+ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics.plugin;
 
@@ -47,19 +47,16 @@ import java.util.Arrays;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Map;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.graph.api.Node;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeRow;
-import org.gephi.data.attributes.api.AttributeType;
+import org.gephi.graph.api.DirectedGraph;
 import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphController;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalDirectedGraph;
-import org.gephi.graph.api.HierarchicalGraph;
 import org.gephi.utils.longtask.spi.LongTask;
 import org.gephi.utils.progress.Progress;
 import org.gephi.utils.progress.ProgressTicket;
@@ -68,16 +65,19 @@ import org.jfree.chart.JFreeChart;
 import org.jfree.chart.plot.PlotOrientation;
 import org.jfree.data.xy.XYSeries;
 import org.jfree.data.xy.XYSeriesCollection;
-import org.openide.util.Lookup;
 import org.gephi.graph.api.NodeIterable;
+import org.openide.util.Lookup;
+
 /**
- * Ref: Matthieu Latapy, Main-memory Triangle Computations for Very Large (Sparse (Power-Law)) Graphs,
- * in Theoretical Computer Science (TCS) 407 (1-3), pages 458-473, 2008
+ * Ref: Matthieu Latapy, Main-memory Triangle Computations for Very Large
+ * (Sparse (Power-Law)) Graphs, in Theoretical Computer Science (TCS) 407 (1-3),
+ * pages 458-473, 2008
  *
  * @author pjmcswee
  */
 class Renumbering implements Comparator<EdgeWrapper> {
 
+    @Override
     public int compare(EdgeWrapper o1, EdgeWrapper o2) {
         if (o1.wrapper.getID() < o2.wrapper.getID()) {
             return -1;
@@ -114,7 +114,9 @@ class ArrayWrapper implements Comparable {
     private int ID;
     public Node node;
 
-    /** Empty Constructor/ */
+    /**
+     * Empty Constructor/
+     */
     ArrayWrapper() {
     }
 
@@ -183,6 +185,7 @@ class ArrayWrapper implements Comparable {
      * @param o
      * @return
      */
+    @Override
     public int compareTo(Object o) {
         ArrayWrapper aw = (ArrayWrapper) o;
         if (aw.length() < length()) {
@@ -202,13 +205,21 @@ class ArrayWrapper implements Comparable {
 public class ClusteringCoefficient implements Statistics, LongTask {
 
     public static final String CLUSTERING_COEFF = "clustering";
-    /** The avergage Clustering Coefficient.*/
+    /**
+     * The avergage Clustering Coefficient.
+     */
     private double avgClusteringCoeff;
-    /**Indicates should treat graph as undirected.*/
+    /**
+     * Indicates should treat graph as undirected.
+     */
     private boolean isDirected;
-    /** Indicates statistics should stop processing/*/
+    /**
+     * Indicates statistics should stop processing/
+     */
     private boolean isCanceled;
-    /** Keeps track of Progress made. */
+    /**
+     * Keeps track of Progress made.
+     */
     private ProgressTicket progress;
     private int[] triangles;
     private ArrayWrapper[] network;
@@ -219,8 +230,8 @@ public class ClusteringCoefficient implements Statistics, LongTask {
 
     public ClusteringCoefficient() {
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            isDirected = graphController.getModel().isDirected();
+        if (graphController != null && graphController.getGraphModel() != null) {
+            isDirected = graphController.getGraphModel().isDirected();
         }
     }
 
@@ -228,82 +239,133 @@ public class ClusteringCoefficient implements Statistics, LongTask {
         return avgClusteringCoeff;
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalGraph hgraph = null;
+        isDirected = graphModel.isDirected();
+
+        Graph hgraph = null;
         if (isDirected) {
-            hgraph = graphModel.getHierarchicalDirectedGraphVisible();
+            hgraph = graphModel.getDirectedGraphVisible();
         } else {
-            hgraph = graphModel.getHierarchicalUndirectedGraphVisible();
+            hgraph = graphModel.getUndirectedGraphVisible();
         }
 
         execute(hgraph, attributeModel);
     }
 
-    public void execute(HierarchicalGraph hgraph, AttributeModel attributeModel) {
+    public void execute(Graph hgraph, AttributeModel attributeModel) {
         isCanceled = false;
 
-        if(isDirected)
-            bruteForce(hgraph, attributeModel);
-        else
-            triangles(hgraph);
-        
+        HashMap<String, Double> resultValues = new HashMap<String, Double>();
+
+        if (isDirected) {
+            avgClusteringCoeff = bruteForce(hgraph, attributeModel);
+        } else {
+            initStartValues(hgraph);
+            resultValues = computeTriangles(hgraph, network, triangles, nodeClustering, isDirected);
+            totalTriangles = resultValues.get("triangles").intValue();
+            avgClusteringCoeff = resultValues.get("clusteringCoefficient");
 
-        //Set results in columns
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn clusteringCol = nodeTable.getColumn(CLUSTERING_COEFF);
-        if (clusteringCol == null) {
-            clusteringCol = nodeTable.addColumn(CLUSTERING_COEFF, "Clustering Coefficient", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
         }
 
-        AttributeColumn triCount = null;
-        if(!isDirected){
+        //Set results in columns
+        Table nodeTable = attributeModel.getNodeTable();
+        Column clusteringCol = nodeTable.getColumn(CLUSTERING_COEFF);
+        if (clusteringCol == null) {
+            clusteringCol = nodeTable.addColumn(CLUSTERING_COEFF, "Clustering Coefficient", Double.class, new Double(0));
+        }
+
+        Column triCount = null;
+        if (!isDirected) {
             triCount = nodeTable.getColumn("Triangles");
             if (triCount == null) {
-                triCount = nodeTable.addColumn("Triangles", "Number of triangles", AttributeType.INT, AttributeOrigin.COMPUTED, new Integer(0));
+                triCount = nodeTable.addColumn("Triangles", "Number of triangles", Integer.class, new Integer(0));
             }
         }
 
         for (int v = 0; v < N; v++) {
             if (network[v].length() > 1) {
-                AttributeRow row = (AttributeRow) network[v].node.getNodeData().getAttributes();
-                row.setValue(clusteringCol, nodeClustering[v]);
-                if(!isDirected)
-                    row.setValue(triCount, triangles[v]);
+                network[v].node.setAttribute(clusteringCol, nodeClustering[v]);
+                if (!isDirected) {
+                    network[v].node.setAttribute(triCount, triangles[v]);
+                }
             }
         }
     }
 
-    private int closest_in_array(int v) {
-        int right = network[v].length() - 1;
+    public void triangles(Graph hgraph) {
+        initStartValues(hgraph);
+        HashMap<String, Double> resultValues = computeTriangles(hgraph, network, triangles,
+                nodeClustering, isDirected);
+        totalTriangles = resultValues.get("triangles").intValue();
+        avgClusteringCoeff = resultValues.get("clusteringCoefficient");
+    }
+
+    public HashMap<String, Double> computeClusteringCoefficient(Graph hgraph, ArrayWrapper[] currentNetwork,
+            int[] currentTriangles, double[] currentNodeClustering, boolean directed) {
+        HashMap<String, Double> resultValues = new HashMap<String, Double>();
+
+        if (isDirected) {
+            double avClusteringCoefficient = bruteForce(hgraph, null);
+            resultValues.put("clusteringCoefficient", avClusteringCoefficient);
+            return resultValues;
+        } else {
+            initStartValues(hgraph);
+            resultValues = computeTriangles(hgraph, currentNetwork, currentTriangles, currentNodeClustering, directed);
+            return resultValues;
+
+        }
+    }
+
+    public void initStartValues(Graph hgraph) {
+        N = hgraph.getNodeCount();
+        K = (int) Math.sqrt(N);
+        nodeClustering = new double[N];
+        network = new ArrayWrapper[N];
+        triangles = new int[N];
+    }
+
+    public int createIndiciesMapAndInitNetwork(Graph hgraph, HashMap<Node, Integer> indicies, ArrayWrapper[] networks, int currentProgress) {
+        int index = 0;
+        for (Node s : hgraph.getNodes()) {
+            indicies.put(s, index);
+            networks[index] = new ArrayWrapper();
+            index++;
+            Progress.progress(progress, ++currentProgress);
+        }
+        return currentProgress;
+    }
+
+    private int closest_in_array(ArrayWrapper[] currentNetwork, int v) {
+        int right = currentNetwork[v].length() - 1;
 
         /* optimization for extreme cases */
         if (right < 0) {
             return (-1);
         }
-        if (network[v].get(0) >= v) {
+        if (currentNetwork[v].get(0) >= v) {
             return (-1);
         }
-        if (network[v].get(right) < v) {
+        if (currentNetwork[v].get(right) < v) {
             return (right);
         }
-        if (network[v].get(right) == v) {
+        if (currentNetwork[v].get(right) == v) {
             return (right - 1);
         }
 
         int left = 0, mid;
         while (right > left) {
             mid = (left + right) / 2;
-            if (v < network[v].get(mid)) {
+            if (v < currentNetwork[v].get(mid)) {
                 right = mid - 1;
-            } else if (v > network[v].get(mid)) {
+            } else if (v > currentNetwork[v].get(mid)) {
                 left = mid + 1;
             } else {
                 return (mid - 1);
             }
         }
 
-
-        if (v > network[v].get(right)) {
+        if (v > currentNetwork[v].get(right)) {
             return (right);
         } else {
 
@@ -315,37 +377,38 @@ public class ClusteringCoefficient implements Statistics, LongTask {
      *
      * @param v - The specific node to count the triangles on.
      */
-    private void newVertex(int v) {
-        int[] A = new int[N];
+    private void newVertex(ArrayWrapper[] currentNetwork, int[] currentTrianlgles, int v, int n) {
+        int[] A = new int[n];
 
-        for (int i = network[v].length() - 1; (i >= 0) && (network[v].get(i) > v); i--) {
-            int neighbor = network[v].get(i);
-            A[neighbor] = network[v].getCount(i);
+        for (int i = currentNetwork[v].length() - 1; (i >= 0) && (currentNetwork[v].get(i) > v); i--) {
+            int neighbor = currentNetwork[v].get(i);
+            A[neighbor] = currentNetwork[v].getCount(i);
         }
-        for (int i = network[v].length() - 1; i >= 0; i--) {
-            int neighbor = network[v].get(i);
-            for (int j = closest_in_array(neighbor); j >= 0; j--) {
-                int next = network[neighbor].get(j);
+        for (int i = currentNetwork[v].length() - 1; i >= 0; i--) {
+            int neighbor = currentNetwork[v].get(i);
+            for (int j = closest_in_array(currentNetwork, neighbor); j >= 0; j--) {
+                int next = currentNetwork[neighbor].get(j);
                 if (A[next] > 0) {
-                    triangles[next] += network[v].getCount(i);
-                    triangles[v] += network[v].getCount(i);
-                    triangles[neighbor] += A[next];
+                    currentTrianlgles[next] += currentNetwork[v].getCount(i);
+                    currentTrianlgles[v] += currentNetwork[v].getCount(i);
+                    currentTrianlgles[neighbor] += A[next];
                 }
             }
         }
     }
 
-    private void tr_link_nohigh(int u, int v, int count) {
+    private void tr_link_nohigh(ArrayWrapper[] currentNetwork, int[] currentTriangles, int u, int v, int count, int k) {
         int iu = 0, iv = 0, w;
-        while ((iu < network[u].length()) && (iv < network[v].length())) {
-            if (network[u].get(iu) < network[v].get(iv)) {
+        while ((iu < currentNetwork[u].length()) && (iv < currentNetwork[v].length())) {
+            if (currentNetwork[u].get(iu) < currentNetwork[v].get(iv)) {
                 iu++;
-            } else if (network[u].get(iu) > network[v].get(iv)) {
+            } else if (currentNetwork[u].get(iu) > currentNetwork[v].get(iv)) {
                 iv++;
             } else { /* neighbor in common */
-                w = network[u].get(iu);
-                if (w >= K) {
-                    triangles[w] += count;
+
+                w = currentNetwork[u].get(iu);
+                if (w >= k) {
+                    currentTriangles[w] += count;
                 }
                 iu++;
                 iv++;
@@ -353,203 +416,272 @@ public class ClusteringCoefficient implements Statistics, LongTask {
         }
     }
 
-    public void triangles(HierarchicalGraph hgraph) {
+    private HashMap<Node, EdgeWrapper> createNeighbourTable(Graph hgraph, Node node, HashMap<Node, Integer> indicies,
+            ArrayWrapper[] networks, boolean directed) {
 
+        HashMap<Node, EdgeWrapper> neighborTable = new HashMap<Node, EdgeWrapper>();
+
+        if (!directed) {
+            for (Edge edge : hgraph.getEdges(node)) {
+                Node neighbor = hgraph.getOpposite(node, edge);
+                neighborTable.put(neighbor, new EdgeWrapper(1, networks[indicies.get(neighbor)]));
+            }
+        } else {
+            for (Node neighbor : ((DirectedGraph) hgraph).getPredecessors(node)) {
+                neighborTable.put(neighbor, new EdgeWrapper(1, networks[indicies.get(neighbor)]));
+            }
+
+            for (Edge out : ((DirectedGraph) hgraph).getOutEdges(node)) {
+                Node neighbor = out.getTarget();
+                EdgeWrapper ew = neighborTable.get(neighbor);
+                if (ew == null) {
+                    neighborTable.put(neighbor, new EdgeWrapper(1, network[indicies.get(neighbor)]));
+                } else {
+                    ew.count++;
+                }
+            }
+        }
+        return neighborTable;
+    }
+
+    private EdgeWrapper[] getEdges(HashMap<Node, EdgeWrapper> neighborTable) {
+
+        int i = 0;
+        EdgeWrapper[] edges = new EdgeWrapper[neighborTable.size()];
+        for (EdgeWrapper e : neighborTable.values()) {
+            edges[i] = e;
+            i++;
+        }
+        return edges;
+    }
+
+    private int processNetwork(ArrayWrapper[] currentNetwork, int currentProgress) {
+        Arrays.sort(currentNetwork);
+        for (int j = 0; j < N; j++) {
+            currentNetwork[j].setID(j);
+            Progress.progress(progress, ++currentProgress);
+        }
+
+        for (int j = 0; j < N; j++) {
+            Arrays.sort(currentNetwork[j].getArray(), new Renumbering());
+            Progress.progress(progress, ++currentProgress);
+        }
+        return currentProgress;
+    }
+
+    private int computeRemainingTrianles(Graph hgraph, ArrayWrapper[] currentNetwork, int[] currentTriangles, int currentProgress) {
+        int n = hgraph.getNodeCount();
+        int k = (int) Math.sqrt(n);
+        for (int v = n - 1; (v >= 0) && (v >= k); v--) {
+            for (int i = closest_in_array(currentNetwork, v); i >= 0; i--) {
+                int u = currentNetwork[v].get(i);
+                if (u >= k) {
+                    tr_link_nohigh(currentNetwork, currentTriangles, u, v, currentNetwork[v].getCount(i), k);
+                }
+            }
+            Progress.progress(progress, ++currentProgress);
+
+            if (isCanceled) {
+                hgraph.readUnlockAll();
+                return currentProgress;
+            }
+        }
+        return currentProgress;
+    }
+
+    private HashMap<String, Double> computeResultValues(Graph hgraph, ArrayWrapper[] currentNetwork,
+            int[] currentTriangles, double[] currentNodeClusterig, boolean directed, int currentProgress) {
+        int n = hgraph.getNodeCount();
+        HashMap<String, Double> totalValues = new HashMap<String, Double>();
+        int numNodesDegreeGreaterThanOne = 0;
+        int trianglesNumber = 0;
+        double currentClusteringCoefficient = 0;
+        for (int v = 0; v < n; v++) {
+            if (currentNetwork[v].length() > 1) {
+                numNodesDegreeGreaterThanOne++;
+                double cc = currentTriangles[v];
+                trianglesNumber += currentTriangles[v];
+                cc /= (currentNetwork[v].length() * (currentNetwork[v].length() - 1));
+                if (!directed) {
+                    cc *= 2.0f;
+                }
+                currentNodeClusterig[v] = cc;
+                currentClusteringCoefficient += cc;
+            }
+            Progress.progress(progress, ++currentProgress);
+
+            if (isCanceled) {
+                hgraph.readUnlockAll();
+                return totalValues;
+            }
+        }
+        trianglesNumber /= 3;
+        currentClusteringCoefficient /= numNodesDegreeGreaterThanOne;
+
+        totalValues.put("triangles", (double) trianglesNumber);
+        totalValues.put("clusteringCoefficient", currentClusteringCoefficient);
+        return totalValues;
+    }
+
+    private HashMap<String, Double> computeTriangles(Graph hgraph, ArrayWrapper[] currentNetwork, int[] currentTriangles,
+            double[] nodeClustering, boolean directed) {
+
+        HashMap<String, Double> resultValues = new HashMap<String, Double>();
         int ProgressCount = 0;
         Progress.start(progress, 7 * hgraph.getNodeCount());
 
         hgraph.readLock();
 
-        N = hgraph.getNodeCount();
-        nodeClustering = new double[N];
+        int n = hgraph.getNodeCount();
 
-        /** Create network for processing */
-        network = new ArrayWrapper[N];
-
-        /**  */
+        /**
+         * Create network for processing
+         */
+        /**
+         *         */
         HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
+
+        ProgressCount = createIndiciesMapAndInitNetwork(hgraph, indicies, currentNetwork, ProgressCount);
+
         int index = 0;
-        for (Node s : hgraph.getNodes()) {
-            indicies.put(s, index);
-            network[index] = new ArrayWrapper();
-            index++;
-            Progress.progress(progress, ++ProgressCount);
-        }
-
-        index = 0;
         for (Node node : hgraph.getNodes()) {
-            HashMap<Node, EdgeWrapper> neighborTable = new HashMap<Node, EdgeWrapper>();
+            HashMap<Node, EdgeWrapper> neighborTable = createNeighbourTable(hgraph, node, indicies, currentNetwork, directed);
 
-            if (!isDirected) {
-                for (Edge edge : hgraph.getEdgesAndMetaEdges(node)) {
-                    Node neighbor = hgraph.getOpposite(node, edge);
-                    neighborTable.put(neighbor, new EdgeWrapper(1, network[indicies.get(neighbor)]));
-                }
-            } else {
-                for (Edge in : ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(node)) {
-                    Node neighbor = in.getSource().getNodeData().getNode(hgraph.getView().getViewId());
-                    neighborTable.put(neighbor, new EdgeWrapper(1, network[indicies.get(neighbor)]));
-                }
-
-                for (Edge out : ((HierarchicalDirectedGraph) hgraph).getOutEdgesAndMetaOutEdges(node)) {
-                    Node neighbor = out.getTarget().getNodeData().getNode(hgraph.getView().getViewId());
-                    EdgeWrapper ew = neighborTable.get(neighbor);
-                    if (ew == null) {
-                        neighborTable.put(neighbor, new EdgeWrapper(1, network[indicies.get(neighbor)]));
-                    } else {
-                        ew.count++;
-                    }
-                }
-            }
-
-            EdgeWrapper[] edges = new EdgeWrapper[neighborTable.size()];
-            int i = 0;
-            for (EdgeWrapper e : neighborTable.values()) {
-                edges[i] = e;
-                i++;
-            }
-            network[index].node = node;
-            network[index].setArray(edges);
+            EdgeWrapper[] edges = getEdges(neighborTable);
+            currentNetwork[index].node = node;
+            currentNetwork[index].setArray(edges);
             index++;
             Progress.progress(progress, ++ProgressCount);
 
             if (isCanceled) {
                 hgraph.readUnlockAll();
-                return;
+                return resultValues;
             }
         }
 
-        Arrays.sort(network);
-        for (int j = 0; j < N; j++) {
-            network[j].setID(j);
-            Progress.progress(progress, ++ProgressCount);
-        }
+        ProgressCount = processNetwork(currentNetwork, ProgressCount);
 
-        for (int j = 0; j < N; j++) {
-            Arrays.sort(network[j].getArray(), new Renumbering());
-            Progress.progress(progress, ++ProgressCount);
-        }
+        int k = (int) Math.sqrt(n);
 
-        triangles = new int[N];
-        K = (int) Math.sqrt(N);
-
-
-        for (int v = 0; v < K && v < N; v++) {
-            newVertex(v);
+        for (int v = 0; v < k && v < n; v++) {
+            newVertex(currentNetwork, currentTriangles, v, n);
             Progress.progress(progress, ++ProgressCount);
         }
 
         /* remaining links */
-        for (int v = N - 1; (v >= 0) && (v >= K); v--) {
-            for (int i = closest_in_array(v); i >= 0; i--) {
-                int u = network[v].get(i);
-                if (u >= K) {
-                    tr_link_nohigh(u, v, network[v].getCount(i));
-                }
-            }
-            Progress.progress(progress, ++ProgressCount);
+        ProgressCount = computeRemainingTrianles(hgraph, currentNetwork, currentTriangles, ProgressCount);
 
-            if (isCanceled) {
-                hgraph.readUnlockAll();
-                return;
-            }
-        }
-
-        //Results and average
-        avgClusteringCoeff = 0;
-        totalTriangles = 0;
-        int numNodesDegreeGreaterThanOne = 0;
-        for (int v = 0; v < N; v++) {
-            if (network[v].length() > 1) {
-                numNodesDegreeGreaterThanOne++;
-                double cc = triangles[v];
-                totalTriangles += triangles[v];
-                cc /= (network[v].length() * (network[v].length() - 1));
-                if (!isDirected) {
-                    cc *= 2.0f;
-                }
-                nodeClustering[v] = cc;
-                avgClusteringCoeff += cc;
-            }
-            Progress.progress(progress, ++ProgressCount);
-
-            if (isCanceled) {
-                hgraph.readUnlockAll();
-                return;
-            }
-        }
-        totalTriangles /= 3;
-        avgClusteringCoeff /= numNodesDegreeGreaterThanOne;
+        resultValues = computeResultValues(hgraph, currentNetwork, currentTriangles, nodeClustering, directed, ProgressCount);
 
         hgraph.readUnlock();
+        return resultValues;
     }
 
-    private void bruteForce(HierarchicalGraph hgraph, AttributeModel attributeModel) {
-    //The atrributes computed by the statistics
-    AttributeTable nodeTable = attributeModel.getNodeTable();
-    AttributeColumn clusteringCol = nodeTable.getColumn("clustering");
-    if (clusteringCol == null) {
-    clusteringCol = nodeTable.addColumn("clustering", "Clustering Coefficient", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
+    private double bruteForce(Graph hgraph, AttributeModel attributeModel) {
+        //The atrributes computed by the statistics
+        Column clusteringColumn = initializeAttributeColunms(attributeModel);
+
+        float totalCC = 0;
+
+        hgraph.readLock();
+
+        Progress.start(progress, hgraph.getNodeCount());
+        int node_count = 0;
+        for (Node node : hgraph.getNodes()) {
+            float nodeClusteringCoefficient = computeNodeClusteringCoefficient(hgraph, node, isDirected);
+
+            if (nodeClusteringCoefficient > -1) {
+
+                saveCalculatedValue(node, clusteringColumn, nodeClusteringCoefficient);
+
+                totalCC += nodeClusteringCoefficient;
+            }
+
+            if (isCanceled) {
+                break;
+            }
+
+            node_count++;
+            Progress.progress(progress, node_count);
+
+        }
+        double clusteringCoeff = totalCC / hgraph.getNodeCount();
+
+        hgraph.readUnlockAll();
+
+        return clusteringCoeff;
     }
-    
-    float totalCC = 0;
-    
-    hgraph.readLock();
-    
-    Progress.start(progress, hgraph.getNodeCount());
-    int node_count = 0;
-    for (Node node : hgraph.getNodes()) {
-    float nodeCC = 0;
-    int neighborhood = 0;
-    NodeIterable neighbors1 = hgraph.getNeighbors(node);
-    for (Node neighbor1 : neighbors1) {
-    neighborhood++;
-    NodeIterable neighbors2 = hgraph.getNeighbors(node);
-    for (Node neighbor2 : neighbors2) {
-    
-    if (neighbor1 == neighbor2) {
-    continue;
+
+    private float increaseCCifNesessary(Graph hgraph, Node neighbor1, Node neighbor2, boolean directed, float nodeCC) {
+        if (neighbor1 == neighbor2) {
+            return nodeCC;
+        }
+        if (directed) {
+            if (hgraph.isAdjacent(neighbor1, neighbor2)) {
+                nodeCC++;
+            }
+            if (hgraph.isAdjacent(neighbor2, neighbor1)) {
+                nodeCC++;
+            }
+        } else {
+            if (hgraph.isAdjacent(neighbor1, neighbor2)) {
+                nodeCC++;
+            }
+        }
+        return nodeCC;
     }
-    if (isDirected) {
-    if (((HierarchicalDirectedGraph) hgraph).getEdge(neighbor1, neighbor2) != null) {
-    nodeCC++;
+
+    private float computeNodeClusteringCoefficient(Graph hgraph, Node node, boolean directed) {
+        float nodeCC = 0;
+        int neighborhood = 0;
+        NodeIterable neighbors1 = hgraph.getNeighbors(node);
+        for (Node neighbor1 : neighbors1) {
+            neighborhood++;
+            NodeIterable neighbors2 = hgraph.getNeighbors(node);
+
+            for (Node neighbor2 : neighbors2) {
+                nodeCC = increaseCCifNesessary(hgraph, neighbor1, neighbor2, directed, nodeCC);
+            }
+        }
+        nodeCC /= 2.0;
+
+        if (neighborhood > 1) {
+            float cc = nodeCC / (.5f * neighborhood * (neighborhood - 1));
+            if (directed) {
+                cc = nodeCC / (neighborhood * (neighborhood - 1));
+            }
+
+            return cc;
+        } else {
+            return -1.f;
+        }
     }
-    if (((HierarchicalDirectedGraph) hgraph).getEdge(neighbor2, neighbor1) != null) {
-    nodeCC++;
+
+    private Column initializeAttributeColunms(AttributeModel attributeModel) {
+
+        if (attributeModel == null) {
+            return null;
+        }
+        Table nodeTable = attributeModel.getNodeTable();
+        Column clusteringCol = nodeTable.getColumn("clustering");
+
+        if (clusteringCol == null) {
+            clusteringCol = nodeTable.addColumn("clustering", "Clustering Coefficient", Double.class, new Double(0));
+        }
+
+        return clusteringCol;
     }
-    } else {
-    if (hgraph.isAdjacent(neighbor1, neighbor2)) {
-    nodeCC++;
-    }
-    }
-    }
-    }
-    nodeCC /= 2.0;
-    
-    if (neighborhood > 1) {
-    float cc = nodeCC / (.5f * neighborhood * (neighborhood - 1));
-    if (isDirected) {
-    cc = nodeCC / (neighborhood * (neighborhood - 1));
-    }
-    
-    AttributeRow row = (AttributeRow) node.getNodeData().getAttributes();
-    row.setValue(clusteringCol, cc);
-    
-    totalCC += cc;
-    }
-    
-    if (isCanceled) {
-    break;
-    }
-    
-    node_count++;
-    Progress.progress(progress, node_count);
-    
-    }
-    avgClusteringCoeff = totalCC / hgraph.getNodeCount();
-    
-    hgraph.readUnlockAll();
+
+    private void saveCalculatedValue(Node node, Column clusteringColumn,
+            float nodeClusteringCoefficient) {
+
+        if (clusteringColumn == null) {
+            return;
+        }
+        node.setAttribute(clusteringColumn, nodeClusteringCoefficient);
     }
+
+    @Override
     public String getReport() {
         //distribution of values
         Map<Double, Integer> dist = new HashMap<Double, Integer>();
@@ -584,20 +716,20 @@ public class ClusteringCoefficient implements Statistics, LongTask {
 
         NumberFormat f = new DecimalFormat("#0.000");
 
-        if(isDirected){
+        if (isDirected) {
             return "<HTML> <BODY> <h1> Clustering Coefficient Metric Report </h1> "
-                + "<hr>"
-                + "<br />" + "<h2> Parameters: </h2>"
-                + "Network Interpretation:  " + (isDirected ? "directed" : "undirected") + "<br />"
-                + "<br>" + "<h2> Results: </h2>"
-                + "Average Clustering Coefficient: " + f.format(avgClusteringCoeff) + "<br />"
-                + "The Average Clustering Coefficient is the mean value of individual coefficients.<br /><br />"
-                + imageFile
-                + "<br /><br />" + "<h2> Algorithm: </h2>"
-                + "Simple and slow brute force.<br />"
-                + "</BODY> </HTML>";
+                    + "<hr>"
+                    + "<br />" + "<h2> Parameters: </h2>"
+                    + "Network Interpretation:  " + (isDirected ? "directed" : "undirected") + "<br />"
+                    + "<br>" + "<h2> Results: </h2>"
+                    + "Average Clustering Coefficient: " + f.format(avgClusteringCoeff) + "<br />"
+                    + "The Average Clustering Coefficient is the mean value of individual coefficients.<br /><br />"
+                    + imageFile
+                    + "<br /><br />" + "<h2> Algorithm: </h2>"
+                    + "Simple and slow brute force.<br />"
+                    + "</BODY> </HTML>";
         } else {
-            
+
             return "<HTML> <BODY> <h1> Clustering Coefficient Metric Report </h1> "
                     + "<hr>"
                     + "<br />" + "<h2> Parameters: </h2>"
@@ -610,7 +742,7 @@ public class ClusteringCoefficient implements Statistics, LongTask {
                     + "<br /><br />" + "<h2> Algorithm: </h2>"
                     + "Matthieu Latapy, <i>Main-memory Triangle Computations for Very Large (Sparse (Power-Law)) Graphs</i>, in Theoretical Computer Science (TCS) 407 (1-3), pages 458-473, 2008<br />"
                     + "</BODY> </HTML>";
-       }
+        }
     }
 
     public void setDirected(boolean isDirected) {
@@ -621,11 +753,13 @@ public class ClusteringCoefficient implements Statistics, LongTask {
         return isDirected;
     }
 
+    @Override
     public boolean cancel() {
         isCanceled = true;
         return true;
     }
 
+    @Override
     public void setProgressTicket(ProgressTicket ProgressTicket) {
         this.progress = ProgressTicket;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/ConnectedComponents.java

@@ -1,67 +1,63 @@
 /*
-Copyright 2008-2011 Gephi
-Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2011 Gephi
+ Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s):
+ Contributor(s):
 
-Portions Copyrighted 2011 Gephi Consortium.
+ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics.plugin;
 
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
-import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedList;
-import java.util.List;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeRow;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeType;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
+import org.gephi.graph.api.DirectedGraph;
 import org.gephi.graph.api.Edge;
 import org.gephi.graph.api.EdgeIterable;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphController;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalDirectedGraph;
-import org.gephi.graph.api.HierarchicalUndirectedGraph;
 import org.gephi.graph.api.Node;
 import org.gephi.graph.api.NodeIterable;
+import org.gephi.graph.api.UndirectedGraph;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.utils.longtask.spi.LongTask;
 import org.gephi.utils.progress.Progress;
@@ -91,49 +87,57 @@ public class ConnectedComponents implements Statistics, LongTask {
 
     public ConnectedComponents() {
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            isDirected = graphController.getModel().isDirected();
+        if (graphController != null && graphController.getGraphModel() != null) {
+            isDirected = graphController.getGraphModel().isDirected();
         }
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
+        isDirected = graphModel.isDirected();
+        isCanceled = false;
+
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraphVisible();
+
+        undirectedGraph.readLock();
 
-        HierarchicalUndirectedGraph undirectedGraph = graphModel.getHierarchicalUndirectedGraphVisible();
         weaklyConnected(undirectedGraph, attributeModel);
         if (isDirected) {
-            HierarchicalDirectedGraph directedGraph = graphModel.getHierarchicalDirectedGraphVisible();
-            top_tarjans(directedGraph, attributeModel);
+            DirectedGraph directedGraph = graphModel.getDirectedGraphVisible();
+            stronglyConnected(directedGraph, attributeModel);
         }
+
+        undirectedGraph.readUnlock();
     }
 
-    public void weaklyConnected(HierarchicalUndirectedGraph hgraph, AttributeModel attributeModel) {
+    public void weaklyConnected(UndirectedGraph graph, AttributeModel attributeModel) {
         isCanceled = false;
-        componentCount = 0;
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn componentCol = nodeTable.getColumn(WEAKLY);
-        if (componentCol == null) {
-            componentCol = nodeTable.addColumn(WEAKLY, "Component ID", AttributeType.INT, AttributeOrigin.COMPUTED, new Integer(0));
-        }
 
-        List<Integer> sizeList = new ArrayList<Integer>();
+        Column componentCol = initializeWeeklyConnectedColumn(attributeModel);
 
-        hgraph.readLock();
+        HashMap<Node, Integer> indicies = createIndiciesMap(graph);
 
-        HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
-        int index = 0;
-        for (Node s : hgraph.getNodes()) {
-            indicies.put(s, index);
-            index++;
-        }
+        LinkedList<LinkedList<Node>> components = computeWeeklyConnectedComponents(graph, indicies);
 
+        saveComputedComponents(components, componentCol);
 
-        int N = hgraph.getNodeCount();
+        fillComponentSizeList(components);
+
+        componentCount = components.size();
+    }
+
+    public LinkedList<LinkedList<Node>> computeWeeklyConnectedComponents(Graph graph, HashMap<Node, Integer> indicies) {
+
+        int N = graph.getNodeCount();
 
         //Keep track of which nodes have been seen
         int[] color = new int[N];
 
-        Progress.start(progress, hgraph.getNodeCount());
+        Progress.start(progress, N);
+
         int seenCount = 0;
+
+        LinkedList<LinkedList<Node>> components = new LinkedList<LinkedList<Node>>();
         while (seenCount < N) {
             //The search Q
             LinkedList<Node> Q = new LinkedList<Node>();
@@ -141,7 +145,7 @@ public class ConnectedComponents implements Statistics, LongTask {
             LinkedList<Node> component = new LinkedList<Node>();
 
             //Seed the seach Q
-            NodeIterable iter = hgraph.getNodes();
+            NodeIterable iter = graph.getNodes();
             for (Node first : iter) {
                 if (color[indicies.get(first)] == 0) {
                     Q.add(first);
@@ -153,19 +157,19 @@ public class ConnectedComponents implements Statistics, LongTask {
             //While there are more nodes to search
             while (!Q.isEmpty()) {
                 if (isCanceled) {
-                    hgraph.readUnlock();
-                    return;
+                    graph.readUnlock();
+                    return new LinkedList<LinkedList<Node>>();
                 }
                 //Get the next Node and add it to the component list
                 Node u = Q.removeFirst();
                 component.add(u);
 
                 //Iterate over all of u's neighbors
-                EdgeIterable edgeIter = hgraph.getEdgesAndMetaEdges(u);
+                EdgeIterable edgeIter = graph.getEdges(u);
 
                 //For each neighbor
                 for (Edge edge : edgeIter) {
-                    Node reachable = hgraph.getOpposite(u, edge);
+                    Node reachable = graph.getOpposite(u, edge);
                     int id = indicies.get(reachable);
                     //If this neighbor is unvisited
                     if (color[id] == 0) {
@@ -180,39 +184,79 @@ public class ConnectedComponents implements Statistics, LongTask {
                 color[indicies.get(u)] = 2;
                 seenCount++;
             }
-            for (Node s : component) {
-                AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
-                row.setValue(componentCol, componentCount);
-            }
-            sizeList.add(component.size());
-            componentCount++;
+            components.add(component);
         }
-        hgraph.readUnlock();
+        return components;
+    }
 
-        componentsSize = new int[sizeList.size()];
-        for (int i = 0; i < sizeList.size(); i++) {
-            componentsSize[i] = sizeList.get(i);
+    private Column initializeWeeklyConnectedColumn(AttributeModel attributeModel) {
+        Table nodeTable = attributeModel.getNodeTable();
+        Column componentCol = nodeTable.getColumn(WEAKLY);
+        if (componentCol == null) {
+            componentCol = nodeTable.addColumn(WEAKLY, "Component ID", Integer.class, new Integer(0));
+        }
+        return componentCol;
+    }
+
+    public HashMap<Node, Integer> createIndiciesMap(Graph hgraph) {
+        HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
+        int index = 0;
+        for (Node s : hgraph.getNodes()) {
+            indicies.put(s, index);
+            index++;
+        }
+        return indicies;
+    }
+
+    private void saveComputedComponents(LinkedList<LinkedList<Node>> components, Column componentCol) {
+        int i = 0;
+        for (LinkedList<Node> component : components) {
+            for (Node s : component) {
+                s.setAttribute(componentCol, i);
+            }
+            i++;
         }
     }
 
-    public void top_tarjans(HierarchicalDirectedGraph hgraph, AttributeModel attributeModel) {
+    void fillComponentSizeList(LinkedList<LinkedList<Node>> components) {
+        componentsSize = new int[components.size()];
+        for (int i = 0; i < components.size(); i++) {
+            componentsSize[i] = components.get(i).size();
+        }
+    }
+
+    private Column initializeStronglyConnectedColumn(AttributeModel attributeModel) {
+        Table nodeTable = attributeModel.getNodeTable();
+        Column componentCol = nodeTable.getColumn(STRONG);
+        if (componentCol == null) {
+            componentCol = nodeTable.addColumn(STRONG, "Strongly-Connected ID", Integer.class, new Integer(0));
+        }
+        return componentCol;
+    }
+
+    public void stronglyConnected(DirectedGraph hgraph, AttributeModel attributeModel) {
         count = 1;
         stronglyCount = 0;
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn componentCol = nodeTable.getColumn(STRONG);
-        if (componentCol == null) {
-            componentCol = nodeTable.addColumn(STRONG, "Strongly-Connected ID", AttributeType.INT, AttributeOrigin.COMPUTED, new Integer(0));
-        }
 
-        hgraph.readLock();
+        Column componentCol = initializeStronglyConnectedColumn(attributeModel);
 
-        HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
-        int v = 0;
-        for (Node s : hgraph.getNodes()) {
-            indicies.put(s, v);
-            v++;
-        }
-        int N = hgraph.getNodeCount();
+        HashMap<Node, Integer> indicies = createIndiciesMap(hgraph);
+
+        LinkedList<LinkedList<Node>> components = top_tarjans(hgraph, indicies);
+
+        saveComputedComponents(components, componentCol);
+
+        stronglyCount = components.size();
+    }
+
+    public LinkedList<LinkedList<Node>> top_tarjans(DirectedGraph graph, HashMap<Node, Integer> indicies) {
+
+        LinkedList<LinkedList<Node>> allComponents = new LinkedList<LinkedList<Node>>();
+
+        count = 1;
+        stronglyCount = 0;
+
+        int N = graph.getNodeCount();
         int[] index = new int[N];
         int[] low_index = new int[N];
 
@@ -223,7 +267,7 @@ public class ConnectedComponents implements Statistics, LongTask {
             //LinkedList<Node> component = new LinkedList<Node>();
             //Seed the seach Q
             Node first = null;
-            NodeIterable iter = hgraph.getNodes();
+            NodeIterable iter = graph.getNodes();
             for (Node u : iter) {
                 if (index[indicies.get(u)] == 0) {
                     first = u;
@@ -232,39 +276,44 @@ public class ConnectedComponents implements Statistics, LongTask {
                 }
             }
             if (first == null) {
-                hgraph.readUnlockAll();
-                return;
+                return allComponents;
+            }
+
+            LinkedList<LinkedList<Node>> components = new LinkedList<LinkedList<Node>>();
+            components = tarjans(components, S, graph, first, index, low_index, indicies);
+            for (LinkedList<Node> component : components) {
+                allComponents.add(component);
             }
-            tarjans(componentCol, S, hgraph, first, index, low_index, indicies);
         }
     }
 
-    private void tarjans(AttributeColumn col, LinkedList<Node> S, HierarchicalDirectedGraph hgraph, Node f, int[] index, int[] low_index, HashMap<Node, Integer> indicies) {
+    private LinkedList<LinkedList<Node>> tarjans(LinkedList<LinkedList<Node>> components, LinkedList<Node> S, DirectedGraph graph, Node f, int[] index, int[] low_index, HashMap<Node, Integer> indicies) {
         int id = indicies.get(f);
         index[id] = count;
         low_index[id] = count;
         count++;
         S.addFirst(f);
-        EdgeIterable edgeIter = hgraph.getOutEdgesAndMetaOutEdges(f);
+        EdgeIterable edgeIter = graph.getOutEdges(f);
         for (Edge e : edgeIter) {
-            Node u = hgraph.getOpposite(f, e);
+            Node u = graph.getOpposite(f, e);
             int x = indicies.get(u);
             if (index[x] == 0) {
-                tarjans(col, S, hgraph, u, index, low_index, indicies);
+                tarjans(components, S, graph, u, index, low_index, indicies);
                 low_index[id] = Math.min(low_index[x], low_index[id]);
             } else if (S.contains(u)) {
                 low_index[id] = Math.min(low_index[id], index[x]);
             }
         }
+        LinkedList<Node> currentComponent = new LinkedList<Node>();
         if (low_index[id] == index[id]) {
             Node v = null;
             while (v != f) {
                 v = S.removeFirst();
-                AttributeRow row = (AttributeRow) v.getNodeData().getAttributes();
-                row.setValue(col, stronglyCount);
+                currentComponent.add(v);
             }
-            stronglyCount++;
+            components.add(currentComponent);
         }
+        return components;
     }
 
     public int getConnectedComponentsCount() {
@@ -296,15 +345,29 @@ public class ConnectedComponents implements Statistics, LongTask {
         return maxIndex;
     }
 
+    public int getComponentNumber(LinkedList<LinkedList<Node>> components, Node node) {
+        int i = 0;
+        for (LinkedList<Node> component : components) {
+            for (Node currentNode : component) {
+                if (currentNode.equals(node)) {
+                    return i;
+                }
+            }
+            i++;
+        }
+        return 0;
+    }
+
+    @Override
     public String getReport() {
         Map<Integer, Integer> sizeDist = new HashMap<Integer, Integer>();
-        for(int v : componentsSize) {
-            if(!sizeDist.containsKey(v)) {
+        for (int v : componentsSize) {
+            if (!sizeDist.containsKey(v)) {
                 sizeDist.put(v, 0);
             }
             sizeDist.put(v, sizeDist.get(v) + 1);
         }
-        
+
         //Distribution series
         XYSeries dSeries = ChartUtils.createXYSeries(sizeDist, "Size Distribution");
 
@@ -327,7 +390,6 @@ public class ConnectedComponents implements Statistics, LongTask {
 
         NumberFormat f = new DecimalFormat("#0.000");
 
-
         String report = "<HTML> <BODY> <h1>Connected Components Report </h1> "
                 + "<hr>"
                 + "<br>"
@@ -336,7 +398,7 @@ public class ConnectedComponents implements Statistics, LongTask {
                 + "<br> <h2> Results: </h2>"
                 + "Number of Weakly Connected Components: " + componentCount + "<br>"
                 + (isDirected ? "Number of Stronlgy Connected Components: " + stronglyCount + "<br>" : "")
-                + "<br /><br />"+imageFile
+                + "<br /><br />" + imageFile
                 + "<br />" + "<h2> Algorithm: </h2>"
                 + "Robert Tarjan, <i>Depth-First Search and Linear Graph Algorithms</i>, in SIAM Journal on Computing 1 (2): 146–160 (1972)<br />"
                 + "</BODY> </HTML>";
@@ -344,11 +406,13 @@ public class ConnectedComponents implements Statistics, LongTask {
         return report;
     }
 
+    @Override
     public boolean cancel() {
         isCanceled = true;
         return true;
     }
 
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
         progress = progressTicket;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/Degree.java

@@ -1,43 +1,43 @@
 /*
-Copyright 2008-2011 Gephi
-Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2011 Gephi
+ Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s):
+ Contributor(s):
 
-Portions Copyrighted 2011 Gephi Consortium.
+ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics.plugin;
 
@@ -45,16 +45,11 @@ import java.text.DecimalFormat;
 import java.text.NumberFormat;
 import java.util.HashMap;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeRow;
-import org.gephi.data.attributes.api.AttributeType;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Table;
 import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalDirectedGraph;
-import org.gephi.graph.api.HierarchicalGraph;
 import org.gephi.graph.api.Node;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.utils.longtask.spi.LongTask;
@@ -74,11 +69,17 @@ public class Degree implements Statistics, LongTask {
     public static final String DEGREE = "degree";
     public static final String AVERAGE_DEGREE = "avgdegree";
     private boolean isDirected; // only set inside this class
-    /** Remembers if the Cancel function has been called. */
+    /**
+     * Remembers if the Cancel function has been called.
+     */
     private boolean isCanceled;
-    /** Keep track of the work done. */
+    /**
+     * Keep track of the work done.
+     */
     private ProgressTicket progress;
-    /**     */
+    /**
+     *
+     */
     private double avgDegree;
     private Map<Integer, Integer> inDegreeDist;
     private Map<Integer, Integer> outDegreeDist;
@@ -96,92 +97,134 @@ public class Degree implements Statistics, LongTask {
      *
      * @param graphModel
      */
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalGraph graph = graphModel.getHierarchicalGraphVisible();
+        Graph graph = graphModel.getGraphVisible();
         execute(graph, attributeModel);
     }
 
-    public void execute(HierarchicalGraph graph, AttributeModel attributeModel) {
-        isDirected = graph instanceof DirectedGraph;
+    public void execute(Graph graph, AttributeModel attributeModel) {
+        isDirected = graph.isDirected();
         isCanceled = false;
-        inDegreeDist = new HashMap<Integer, Integer>();
-        outDegreeDist = new HashMap<Integer, Integer>();
-        degreeDist = new HashMap<Integer, Integer>();
 
-        //Attributes cols
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeTable graphTable = attributeModel.getGraphTable();
-        AttributeColumn inCol = nodeTable.getColumn(INDEGREE);
-        AttributeColumn outCol = nodeTable.getColumn(OUTDEGREE);
-        AttributeColumn degCol = nodeTable.getColumn(DEGREE);
-        AttributeColumn avgDegreeCol = graphTable.getColumn(AVERAGE_DEGREE);
-        if (isDirected) {
-            if (inCol == null) {
-                inCol = nodeTable.addColumn(INDEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.InDegree"), AttributeType.INT, AttributeOrigin.COMPUTED, 0);
-            }
-            if (outCol == null) {
-                outCol = nodeTable.addColumn(OUTDEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.OutDegree"), AttributeType.INT, AttributeOrigin.COMPUTED, 0);
-            }
-        }
-        if (degCol == null) {
-            degCol = nodeTable.addColumn(DEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.Degree"), AttributeType.INT, AttributeOrigin.COMPUTED, 0);
-        }
-        if(avgDegreeCol == null) {
-            avgDegreeCol = graphTable.addColumn(AVERAGE_DEGREE, NbBundle.getMessage(Degree.class, "Degree.graphcolumn.AverageDegree"), AttributeType.DOUBLE, AttributeOrigin.COMPUTED, 0.0);
-        }
-
-        int i = 0;
+        initializeDegreeDists();
+        initializeAttributeColunms(attributeModel);
 
         graph.readLock();
 
-        Progress.start(progress, graph.getNodeCount());
-        
-        HierarchicalDirectedGraph directedGraph = null;
-        if(isDirected) {
-            directedGraph = graph.getGraphModel().getHierarchicalDirectedGraphVisible();
+        avgDegree = calculateAverageDegree(graph, isDirected, true);
+
+        graph.setAttribute(AVERAGE_DEGREE, avgDegree);
+
+        graph.readUnlockAll();
+    }
+
+    protected int calculateInDegree(DirectedGraph directedGraph, Node n) {
+        return directedGraph.getInDegree(n);
+    }
+
+    protected int calculateOutDegree(DirectedGraph directedGraph, Node n) {
+        return directedGraph.getOutDegree(n);
+    }
+
+    protected int calculateDegree(Graph graph, Node n) {
+        return graph.getDegree(n);
+    }
+
+    protected double calculateAverageDegree(Graph graph, boolean isDirected, boolean updateAttributes) {
+        double averageDegree = 0;
+
+        DirectedGraph directedGraph = null;
+
+        if (isDirected) {
+            directedGraph = (DirectedGraph) graph;
         }
 
+        Progress.start(progress, graph.getNodeCount());
+
         for (Node n : graph.getNodes()) {
-            AttributeRow row = (AttributeRow) n.getNodeData().getAttributes();
+            int inDegree = 0;
+            int outDegree = 0;
+            int degree = 0;
             if (isDirected) {
-                int inDegree = directedGraph.getTotalInDegree(n);
-                int outDegree = directedGraph.getTotalOutDegree(n);
-                row.setValue(inCol, inDegree);
-                row.setValue(outCol, outDegree);
-                if (!inDegreeDist.containsKey(inDegree)) {
-                    inDegreeDist.put(inDegree, 0);
-                }
-                inDegreeDist.put(inDegree, inDegreeDist.get(inDegree) + 1);
-                if (!outDegreeDist.containsKey(outDegree)) {
-                    outDegreeDist.put(outDegree, 0);
-                }
-                outDegreeDist.put(outDegree, outDegreeDist.get(outDegree) + 1);
+                inDegree = calculateInDegree(directedGraph, n);
+                outDegree = calculateOutDegree(directedGraph, n);
             }
-            int degree = graph.getTotalDegree(n);
-            row.setValue(degCol, degree);
-            avgDegree += degree;
-            if (!degreeDist.containsKey(degree)) {
-                degreeDist.put(degree, 0);
+            degree = calculateDegree(graph, n);
+
+            if (updateAttributes) {
+                n.setAttribute(DEGREE, degree);
+                if (isDirected) {
+                    n.setAttribute(INDEGREE, inDegree);
+                    n.setAttribute(OUTDEGREE, outDegree);
+                    updateDegreeDists(inDegree, outDegree, degree);
+                } else {
+                    updateDegreeDists(degree);
+
+                }
             }
-            degreeDist.put(degree, degreeDist.get(degree) + 1);
+
+            averageDegree += degree;
 
             if (isCanceled) {
                 break;
             }
-            i++;
-            Progress.progress(progress, i);
+            Progress.progress(progress);
         }
 
-        avgDegree /= graph.getNodeCount();
-        graph.getAttributes().setValue(avgDegreeCol.getIndex(), avgDegree);
+        averageDegree /= graph.getNodeCount();
 
-        graph.readUnlockAll();
+        return averageDegree;
+    }
+
+    private void initializeAttributeColunms(AttributeModel attributeModel) {
+        Table nodeTable = attributeModel.getNodeTable();
+        if (isDirected) {
+            if (!nodeTable.hasColumn(INDEGREE)) {
+                nodeTable.addColumn(INDEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.InDegree"), Integer.class, 0);
+            }
+            if (!nodeTable.hasColumn(OUTDEGREE)) {
+                nodeTable.addColumn(OUTDEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.OutDegree"), Integer.class, 0);
+            }
+        }
+        if (!nodeTable.hasColumn(DEGREE)) {
+            nodeTable.addColumn(DEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.Degree"), Integer.class, 0);
+        }
+    }
+
+    private void initializeDegreeDists() {
+        inDegreeDist = new HashMap<Integer, Integer>();
+        outDegreeDist = new HashMap<Integer, Integer>();
+        degreeDist = new HashMap<Integer, Integer>();
+    }
+
+    private void updateDegreeDists(int inDegree, int outDegree, int degree) {
+        if (!inDegreeDist.containsKey(inDegree)) {
+            inDegreeDist.put(inDegree, 0);
+        }
+        inDegreeDist.put(inDegree, inDegreeDist.get(inDegree) + 1);
+        if (!outDegreeDist.containsKey(outDegree)) {
+            outDegreeDist.put(outDegree, 0);
+        }
+        outDegreeDist.put(outDegree, outDegreeDist.get(outDegree) + 1);
+        if (!degreeDist.containsKey(degree)) {
+            degreeDist.put(degree, 0);
+        }
+        degreeDist.put(degree, degreeDist.get(degree) + 1);
+    }
+
+    private void updateDegreeDists(int degree) {
+        if (!degreeDist.containsKey(degree)) {
+            degreeDist.put(degree, 0);
+        }
+        degreeDist.put(degree, degreeDist.get(degree) + 1);
     }
 
     /**
      *
      * @return
      */
+    @Override
     public String getReport() {
         String report = "";
         if (isDirected) {
@@ -213,7 +256,7 @@ public class Degree implements Statistics, LongTask {
                     + "<hr>"
                     + "<br> <h2> Results: </h2>"
                     + "Average Degree: " + f.format(avgDegree)
-                    + "<br /><br />"+degreeImageFile
+                    + "<br /><br />" + degreeImageFile
                     + "</BODY></HTML>";
         }
         return report;
@@ -275,18 +318,18 @@ public class Degree implements Statistics, LongTask {
         ChartUtils.decorateChart(chart3);
         ChartUtils.scaleChart(chart3, dSeries, false);
         String outdegreeImageFile = ChartUtils.renderChart(chart3, "outdegree-distribution.png");
-        
+
         NumberFormat f = new DecimalFormat("#0.000");
 
         String report = "<HTML> <BODY> <h1>Degree Report </h1> "
                 + "<hr>"
                 + "<br> <h2> Results: </h2>"
                 + "Average Degree: " + f.format(avgDegree)
-                + "<br /><br />"+degreeImageFile
-                + "<br /><br />"+indegreeImageFile
-                + "<br /><br />"+outdegreeImageFile
+                + "<br /><br />" + degreeImageFile
+                + "<br /><br />" + indegreeImageFile
+                + "<br /><br />" + outdegreeImageFile
                 + "</BODY></HTML>";
-        
+
         return report;
     }
 
@@ -294,6 +337,7 @@ public class Degree implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public boolean cancel() {
         this.isCanceled = true;
         return true;
@@ -303,6 +347,7 @@ public class Degree implements Statistics, LongTask {
      *
      * @param progressTicket
      */
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
         this.progress = progressTicket;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/EigenvectorCentrality.java

@@ -1,61 +1,57 @@
 /*
-Copyright 2008-2011 Gephi
-Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2011 Gephi
+ Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s):
+ Contributor(s):
 
-Portions Copyrighted 2011 Gephi Consortium.
+ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics.plugin;
 
 import java.util.HashMap;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeRow;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeType;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
+import org.gephi.graph.api.DirectedGraph;
 import org.gephi.graph.api.Edge;
 import org.gephi.graph.api.EdgeIterable;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphController;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalDirectedGraph;
-import org.gephi.graph.api.HierarchicalGraph;
-import org.gephi.graph.api.HierarchicalUndirectedGraph;
 import org.gephi.graph.api.Node;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.utils.longtask.spi.LongTask;
@@ -79,14 +75,16 @@ public class EigenvectorCentrality implements Statistics, LongTask {
     private double[] centralities;
     private double sumChange;
     private ProgressTicket progress;
-    /** */
+    /**
+     *
+     */
     private boolean isCanceled;
     private boolean isDirected;
 
     public EigenvectorCentrality() {
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            isDirected = graphController.getModel().isDirected();
+        if (graphController != null && graphController.getGraphModel() != null) {
+            isDirected = graphController.getGraphModel().isDirected();
         }
     }
 
@@ -95,7 +93,7 @@ public class EigenvectorCentrality implements Statistics, LongTask {
     }
 
     /**
-     * 
+     *
      * @return
      */
     public int getNumRuns() {
@@ -103,7 +101,7 @@ public class EigenvectorCentrality implements Statistics, LongTask {
     }
 
     /**
-     * 
+     *
      * @return
      */
     public boolean isDirected() {
@@ -111,7 +109,7 @@ public class EigenvectorCentrality implements Statistics, LongTask {
     }
 
     /**
-     * 
+     *
      * @param isDirected
      */
     public void setDirected(boolean isDirected) {
@@ -123,97 +121,151 @@ public class EigenvectorCentrality implements Statistics, LongTask {
      * @param graphModel
      * @param attributeModel
      */
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalGraph graph = null;
+        isDirected = graphModel.isDirected();
+        isCanceled = false;
+
+        Graph graph;
         if (isDirected) {
-            graph = graphModel.getHierarchicalDirectedGraphVisible();
+            graph = graphModel.getDirectedGraphVisible();
         } else {
-            graph = graphModel.getHierarchicalUndirectedGraphVisible();
+            graph = graphModel.getUndirectedGraphVisible();
         }
         execute(graph, attributeModel);
     }
 
-    public void execute(HierarchicalGraph hgraph, AttributeModel attributeModel) {
+    public void execute(Graph hgraph, AttributeModel attributeModel) {
 
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn eigenCol = nodeTable.getColumn(EIGENVECTOR);
-        if (eigenCol == null) {
-            eigenCol = nodeTable.addColumn(EIGENVECTOR, "Eigenvector Centrality", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
-        }
+        Column column = initializeAttributeColunms(attributeModel);
 
         int N = hgraph.getNodeCount();
         hgraph.readLock();
 
-        double[] tmp = new double[N];
         centralities = new double[N];
 
         Progress.start(progress, numRuns);
 
         HashMap<Integer, Node> indicies = new HashMap<Integer, Node>();
         HashMap<Node, Integer> invIndicies = new HashMap<Node, Integer>();
-        int count = 0;
-        for (Node u : hgraph.getNodes()) {
-            indicies.put(count, u);
-            invIndicies.put(u, count);
-            centralities[count] = 1;
-            count++;
-        }
-        for (int s = 0; s < numRuns; s++) {
-            double max = 0;
-            for (int i = 0; i < N; i++) {
-                Node u = indicies.get(i);
-                EdgeIterable iter = null;
-                if (isDirected) {
-                    iter = ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(u);
-                } else {
-                    iter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(u);
-                }
+        fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
 
-                for (Edge e : iter) {
-                    Node v = hgraph.getOpposite(u, e);
-                    Integer id = invIndicies.get(v);
-                    tmp[i] += centralities[id];
-                }
-                max = Math.max(max, tmp[i]);
-                if (isCanceled) {
-                    return;
-                }
-            }
-            sumChange = 0;
-            for (int k = 0; k < N; k++) {
-                if (max != 0) {
-                    sumChange += Math.abs(centralities[k] - (tmp[k] / max));
-                    centralities[k] = tmp[k] / max;
-                    //tmp[k] = 0;
-                }
-                if (isCanceled) {
-                    return;
-                }
-            }
-            if (isCanceled) {
-                return;
-            }
+        sumChange = calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, isDirected, numRuns);
 
-            Progress.progress(progress);
-        }
+        saveCalculatedValues(hgraph, column, indicies, centralities);
 
-        for (int i = 0; i < N; i++) {
-            Node s = indicies.get(i);
-            AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
-            row.setValue(eigenCol, centralities[i]);
-            if (isCanceled) {
-                return;
-            }
-        }
         hgraph.readUnlock();
 
         Progress.finish(progress);
     }
 
+    private Column initializeAttributeColunms(AttributeModel attributeModel) {
+        Table nodeTable = attributeModel.getNodeTable();
+        Column eigenCol = nodeTable.getColumn(EIGENVECTOR);
+        if (eigenCol == null) {
+            eigenCol = nodeTable.addColumn(EIGENVECTOR, "Eigenvector Centrality", Double.class, new Double(0));
+        }
+        return eigenCol;
+    }
+
+    private void saveCalculatedValues(Graph hgraph, Column attributeColumn, HashMap<Integer, Node> indicies,
+            double[] eigCenrtalities) {
+
+        int N = hgraph.getNodeCount();
+
+        for (int i = 0; i < N; i++) {
+            Node s = indicies.get(i);
+
+            s.setAttribute(attributeColumn, eigCenrtalities[i]);
+        }
+    }
+
+    public void fillIndiciesMaps(Graph hgraph, double[] eigCentralities, HashMap<Integer, Node> indicies, HashMap<Node, Integer> invIndicies) {
+        if (indicies == null || invIndicies == null) {
+            return;
+        }
+
+        int count = 0;
+        for (Node u : hgraph.getNodes()) {
+            indicies.put(count, u);
+            invIndicies.put(u, count);
+            eigCentralities[count] = 1;
+            count++;
+        }
+    }
+
+    private double computeMaxValueAndTempValues(Graph hgraph, HashMap<Integer, Node> indicies, HashMap<Node, Integer> invIndicies,
+            double[] tempValues, double[] centralityValues, boolean directed) {
+
+        double max = 0.;
+        int N = hgraph.getNodeCount();
+
+        for (int i = 0; i < N; i++) {
+            Node u = indicies.get(i);
+            EdgeIterable iter = null;
+            if (directed) {
+                iter = ((DirectedGraph) hgraph).getInEdges(u);
+            } else {
+                iter = hgraph.getEdges(u);
+            }
+
+            for (Edge e : iter) {
+                Node v = hgraph.getOpposite(u, e);
+                Integer id = invIndicies.get(v);
+                tempValues[i] += centralityValues[id];
+            }
+            max = Math.max(max, tempValues[i]);
+            if (isCanceled) {
+                return max;
+            }
+        }
+
+        return max;
+    }
+
+    private double updateValues(Graph hgraph, double[] tempValues, double[] centralityValues, double max) {
+        double sumChanged = 0.;
+        int N = hgraph.getNodeCount();
+
+        for (int k = 0; k < N; k++) {
+            if (max != 0) {
+                sumChanged += Math.abs(centralityValues[k] - (tempValues[k] / max));
+                centralityValues[k] = tempValues[k] / max;
+            }
+            if (isCanceled) {
+                return sumChanged;
+            }
+        }
+
+        return sumChanged;
+    }
+
+    public double calculateEigenvectorCentrality(Graph hgraph, double[] eigCentralities,
+            HashMap<Integer, Node> indicies, HashMap<Node, Integer> invIndicies,
+            boolean directed, int numIterations) {
+
+        int N = hgraph.getNodeCount();
+        double sumChanged = 0.;
+        double[] tmp = new double[N];
+
+        for (int s = 0; s < numIterations; s++) {
+            double max = computeMaxValueAndTempValues(hgraph, indicies, invIndicies, tmp, eigCentralities, directed);
+            sumChanged = updateValues(hgraph, tmp, eigCentralities, max);
+            if (isCanceled) {
+                return sumChanged;
+            }
+
+            Progress.progress(progress);
+        }
+
+        return sumChanged;
+    }
+
     /**
-     * 
+     *
      * @return
      */
+    @Override
     public String getReport() {
         //distribution of values
         Map<Double, Integer> dist = new HashMap<Double, Integer>();
@@ -246,7 +298,7 @@ public class EigenvectorCentrality implements Statistics, LongTask {
         ChartUtils.decorateChart(chart);
         ChartUtils.scaleChart(chart, dSeries, true);
         String imageFile = ChartUtils.renderChart(chart, "eigenvector-centralities.png");
-        
+
         String report = "<HTML> <BODY> <h1>Eigenvector Centrality Report</h1> "
                 + "<hr>"
                 + "<h2> Parameters: </h2>"
@@ -261,11 +313,13 @@ public class EigenvectorCentrality implements Statistics, LongTask {
 
     }
 
+    @Override
     public boolean cancel() {
         this.isCanceled = true;
         return true;
     }
 
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
         this.progress = progressTicket;
 

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/GraphDensity.java

@@ -43,10 +43,10 @@ package org.gephi.statistics.plugin;
 
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
-import org.gephi.data.attributes.api.AttributeModel;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphController;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalGraph;
 import org.gephi.statistics.spi.Statistics;
 import org.openide.util.Lookup;
 
@@ -63,8 +63,8 @@ public class GraphDensity implements Statistics {
 
     public GraphDensity() {
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            isDirected = graphController.getModel().isDirected();
+        if (graphController != null && graphController.getGraphModel()!= null) {
+            isDirected = graphController.getGraphModel().isDirected();
         }
     }
 
@@ -80,29 +80,37 @@ public class GraphDensity implements Statistics {
         return density;
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalGraph hgraph;
-
+        Graph graph;
         if (isDirected) {
-            hgraph = graphModel.getHierarchicalDirectedGraphVisible();
+            graph = graphModel.getDirectedGraphVisible();
         } else {
-            hgraph = graphModel.getHierarchicalUndirectedGraphVisible();
+            graph = graphModel.getUndirectedGraphVisible();
         }
+        
+        density = calculateDensity(graph, isDirected);
+    }
+    
+    public double calculateDensity(Graph graph, boolean isGraphDirected) {
+        double result;
 
-        double edgesCount = hgraph.getTotalEdgeCount();
-        double nodesCount = hgraph.getNodeCount();
+        double edgesCount = graph.getEdgeCount();
+        double nodesCount = graph.getNodeCount();
         double multiplier = 1;
 
-        if (!isDirected) {
+        if (!isGraphDirected) {
             multiplier = 2;
         }
-        density = (multiplier * edgesCount) / (nodesCount * nodesCount - nodesCount);
+        result = (multiplier * edgesCount) / (nodesCount * nodesCount - nodesCount);
+        return result;
     }
 
     /**
      *
      * @return
      */
+    @Override
     public String getReport() {
         NumberFormat f = new DecimalFormat("#0.000");
 

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/GraphDistance.java

@@ -1,44 +1,44 @@
 /*
-Copyright 2008-2011 Gephi
-Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2011 Gephi
+ Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s):
+ Contributor(s):
 
-Portions Copyrighted 2011 Gephi Consortium.
-*/
+ Portions Copyrighted 2011 Gephi Consortium.
+ */
 package org.gephi.statistics.plugin;
 
 import java.io.IOException;
@@ -49,12 +49,9 @@ import java.util.LinkedList;
 import java.util.ListIterator;
 import java.util.Map;
 import java.util.Stack;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeRow;
-import org.gephi.data.attributes.api.AttributeType;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
 import org.gephi.utils.TempDirUtils;
 import org.gephi.utils.TempDirUtils.TempDir;
 import org.gephi.utils.longtask.spi.LongTask;
@@ -67,10 +64,11 @@ import org.jfree.data.xy.XYSeries;
 import org.jfree.data.xy.XYSeriesCollection;
 import org.openide.util.Exceptions;
 import org.openide.util.Lookup;
+import org.openide.util.NbBundle;
 
 /**
- * Ref: Ulrik Brandes, A Faster Algorithm for Betweenness Centrality,
- * in Journal of Mathematical Sociology 25(2):163-177, (2001)
+ * Ref: Ulrik Brandes, A Faster Algorithm for Betweenness Centrality, in Journal
+ * of Mathematical Sociology 25(2):163-177, (2001)
  *
  * @author pjmcswee
  */
@@ -79,113 +77,129 @@ public class GraphDistance implements Statistics, LongTask {
     public static final String BETWEENNESS = "betweenesscentrality";
     public static final String CLOSENESS = "closnesscentrality";
     public static final String ECCENTRICITY = "eccentricity";
-    /** */
+    /**
+     *      */
     private double[] betweenness;
-    /** */
+    /**
+     *      */
     private double[] closeness;
-    /** */
+    /**
+     *      */
     private double[] eccentricity;
-    /** */
+    /**
+     *      */
     private int diameter;
     private int radius;
-    /** */
+    /**
+     *      */
     private double avgDist;
-    /** */
+    /**
+     *      */
     private int N;
-    /** */
+    /**
+     *      */
     private boolean isDirected;
-    /** */
+    /**
+     *      */
     private ProgressTicket progress;
-    /** */
+    /**
+     *      */
     private boolean isCanceled;
     private int shortestPaths;
     private boolean isNormalized;
 
-    public GraphDistance() {
-        GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            isDirected = graphController.getModel().isDirected();
-        }
-    }
-
     public double getPathLength() {
         return avgDist;
     }
 
     /**
-     * 
+     *
      * @return
      */
     public double getDiameter() {
         return diameter;
     }
+    
+    public double getRadius() {
+        return radius;
+    }
 
+    public GraphDistance() {
+        GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
+        if (graphController != null && graphController.getGraphModel() != null) {
+            isDirected = graphController.getGraphModel().isDirected();
+        }
+    }
+    
     /**
      *
      * @param graphModel
+     * @param attributeModel
      */
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalGraph graph = null;
+        isDirected = graphModel.isDirected();
+
+        Graph graph = null;
         if (isDirected) {
-            graph = graphModel.getHierarchicalDirectedGraphVisible();
+            graph = graphModel.getDirectedGraphVisible();
         } else {
-            graph = graphModel.getHierarchicalUndirectedGraphVisible();
+            graph = graphModel.getUndirectedGraphVisible();
         }
         execute(graph, attributeModel);
     }
 
-    public void execute(HierarchicalGraph hgraph, AttributeModel attributeModel) {
+    public void execute(Graph hgraph, AttributeModel attributeModel) {
         isCanceled = false;
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn eccentricityCol = nodeTable.getColumn(ECCENTRICITY);
-        AttributeColumn closenessCol = nodeTable.getColumn(CLOSENESS);
-        AttributeColumn betweenessCol = nodeTable.getColumn(BETWEENNESS);
-        if (eccentricityCol == null) {
-            eccentricityCol = nodeTable.addColumn(ECCENTRICITY, "Eccentricity", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
-        }
-        if (closenessCol == null) {
-            closenessCol = nodeTable.addColumn(CLOSENESS, "Closeness Centrality", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
-        }
-        if (betweenessCol == null) {
-            betweenessCol = nodeTable.addColumn(BETWEENNESS, "Betweenness Centrality", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
-        }
+        
+        initializeAttributeColunms(attributeModel); 
 
         hgraph.readLock();
 
         N = hgraph.getNodeCount();
+        
+        initializeStartValues();
+        
+        HashMap<Node, Integer> indicies = createIndiciesMap(hgraph);
 
-        betweenness = new double[N];
-        eccentricity = new double[N];
-        closeness = new double[N];
-        diameter = 0;
-        avgDist = 0;
-        shortestPaths = 0;
-        radius = Integer.MAX_VALUE;
-        HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
-        int index = 0;
-        for (Node s : hgraph.getNodes()) {
-            indicies.put(s, index);
-            index++;
-        }
-
+        Map<String, double[]> metrics = calculateDistanceMetrics(hgraph, indicies, isDirected, isNormalized);
+        
+        eccentricity = metrics.get(ECCENTRICITY);
+        closeness = metrics.get(CLOSENESS);
+        betweenness = metrics.get(BETWEENNESS);
+        
+        saveCalculatedValues(hgraph, indicies, eccentricity, betweenness, closeness);
+                
+        hgraph.readUnlock();
+    }
+    
+    public Map<String, double[]> calculateDistanceMetrics(Graph hgraph, HashMap<Node, Integer> indicies, boolean directed, boolean normalized) {
+        int n = hgraph.getNodeCount();
+        
+        HashMap<String, double[]> metrics = new HashMap<String, double[]>();
+        
+        double[] nodeEccentricity = new double[n];
+        double[] nodeBetweenness = new double[n];
+        double[] nodeCloseness = new double[n];
+        
+        metrics.put(ECCENTRICITY, nodeEccentricity);
+        metrics.put(CLOSENESS, nodeCloseness);
+        metrics.put(BETWEENNESS, nodeBetweenness);
+        
         Progress.start(progress, hgraph.getNodeCount());
         int count = 0;
+        
+        
         for (Node s : hgraph.getNodes()) {
             Stack<Node> S = new Stack<Node>();
 
-            LinkedList<Node>[] P = new LinkedList[N];
-            double[] theta = new double[N];
-            int[] d = new int[N];
-            for (int j = 0; j < N; j++) {
-                P[j] = new LinkedList<Node>();
-                theta[j] = 0;
-                d[j] = -1;
-            }
-
+            LinkedList<Node>[] P = new LinkedList[n];
+            double[] theta = new double[n];
+            int[] d = new int[n];
+            
             int s_index = indicies.get(s);
-
-            theta[s_index] = 1;
-            d[s_index] = 0;
+            
+            setInitParametetrsForNode(s, P, theta, d, s_index, n);
 
             LinkedList<Node> Q = new LinkedList<Node>();
             Q.addLast(s);
@@ -194,12 +208,7 @@ public class GraphDistance implements Statistics, LongTask {
                 S.push(v);
                 int v_index = indicies.get(v);
 
-                EdgeIterable edgeIter = null;
-                if (isDirected) {
-                    edgeIter = ((HierarchicalDirectedGraph) hgraph).getOutEdgesAndMetaOutEdges(v);
-                } else {
-                    edgeIter = hgraph.getEdgesAndMetaEdges(v);
-                }
+                EdgeIterable edgeIter = getEdgeIter(hgraph, v, directed);
 
                 for (Edge edge : edgeIter) {
                     Node reachable = hgraph.getOpposite(v, edge);
@@ -216,25 +225,25 @@ public class GraphDistance implements Statistics, LongTask {
                 }
             }
             double reachable = 0;
-            for (int i = 0; i < N; i++) {
+            for (int i = 0; i < n; i++) {
                 if (d[i] > 0) {
                     avgDist += d[i];
-                    eccentricity[s_index] = (int) Math.max(eccentricity[s_index], d[i]);
-                    closeness[s_index] += d[i];
+                    nodeEccentricity[s_index] = (int) Math.max(nodeEccentricity[s_index], d[i]);
+                    nodeCloseness[s_index] += d[i];
                     diameter = Math.max(diameter, d[i]);
                     reachable++;
                 }
             }
 
-            radius = (int) Math.min(eccentricity[s_index], radius);
+            radius = (int) Math.min(nodeEccentricity[s_index], radius);
 
             if (reachable != 0) {
-                closeness[s_index] /= reachable;
+                nodeCloseness[s_index] /= reachable;
             }
 
             shortestPaths += reachable;
 
-            double[] delta = new double[N];
+            double[] delta = new double[n];
             while (!S.empty()) {
                 Node w = S.pop();
                 int w_index = indicies.get(w);
@@ -245,35 +254,105 @@ public class GraphDistance implements Statistics, LongTask {
                     delta[u_index] += (theta[u_index] / theta[w_index]) * (1 + delta[w_index]);
                 }
                 if (w != s) {
-                    betweenness[w_index] += delta[w_index];
+                    nodeBetweenness[w_index] += delta[w_index];
                 }
             }
             count++;
             if (isCanceled) {
                 hgraph.readUnlockAll();
-                return;
+                return metrics;
             }
             Progress.progress(progress, count);
         }
 
         avgDist /= shortestPaths;//mN * (mN - 1.0f);
 
+        calculateCorrection(hgraph, indicies, nodeBetweenness, nodeCloseness, directed, normalized);
+        
+        return metrics;
+    }
+    
+    private void setInitParametetrsForNode(Node s, LinkedList<Node>[] P, double[] theta, int[] d, int index, int n) {           
+            for (int j = 0; j < n; j++) {
+                P[j] = new LinkedList<Node>();
+                theta[j] = 0;
+                d[j] = -1;
+            }
+            theta[index] = 1;
+            d[index] = 0;
+    }
+    
+    private EdgeIterable getEdgeIter(Graph hgraph, Node v, boolean directed) {
+            EdgeIterable edgeIter = null;
+            if (directed) {
+                edgeIter = ((DirectedGraph) hgraph).getOutEdges(v);
+            } else {
+                edgeIter = hgraph.getEdges(v);
+             }
+            return edgeIter;
+    }
+    
+    private void initializeAttributeColunms(AttributeModel attributeModel) {
+        Table nodeTable = attributeModel.getNodeTable();
+        if (!nodeTable.hasColumn(ECCENTRICITY)) {
+            nodeTable.addColumn(ECCENTRICITY, "Eccentricity", Double.class, new Double(0));
+        }
+        if (!nodeTable.hasColumn(CLOSENESS)) {
+            nodeTable.addColumn(CLOSENESS, "Closeness Centrality", Double.class, new Double(0));
+        }
+        if (!nodeTable.hasColumn(BETWEENNESS)) {
+            nodeTable.addColumn(BETWEENNESS, "Betweenness Centrality", Double.class, new Double(0));
+        }
+    }
+    
+     public  HashMap<Node, Integer> createIndiciesMap(Graph hgraph) {
+       HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
+        int index = 0;
+        for (Node s : hgraph.getNodes()) {
+            indicies.put(s, index);
+            index++;
+        } 
+        return indicies;
+    }
+     
+     public void initializeStartValues() {
+        betweenness = new double[N];
+        eccentricity = new double[N];
+        closeness = new double[N];
+        diameter = 0;
+        avgDist = 0;
+        shortestPaths = 0;
+        radius = Integer.MAX_VALUE;
+     }
+     
+     private void calculateCorrection(Graph hgraph, HashMap<Node, Integer> indicies,
+             double[] nodeBetweenness, double[] nodeCloseness, boolean directed, boolean normalized) {
+         
+         int n = hgraph.getNodeCount();
+         
+         for (Node s : hgraph.getNodes()) {
+            
+             int s_index = indicies.get(s);
+
+            if (!directed) {
+                nodeBetweenness[s_index] /= 2;
+            }
+            if (normalized) {
+                nodeCloseness[s_index] = (nodeCloseness[s_index] == 0) ? 0 : 1.0 / nodeCloseness[s_index];
+                nodeBetweenness[s_index] /= directed ? (n - 1) * (n - 2) : (n - 1) * (n - 2) / 2;
+            }     
+         }
+     }
+     
+     private void saveCalculatedValues(Graph hgraph, HashMap<Node, Integer> indicies,
+            double[] nodeEccentricity, double[] nodeBetweenness, double[] nodeCloseness) {
         for (Node s : hgraph.getNodes()) {
-            AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
             int s_index = indicies.get(s);
 
-            if (!isDirected) {
-                betweenness[s_index] /= 2;
-            }
-            if (isNormalized) {
-                closeness[s_index] = (closeness[s_index] == 0) ? 0 : 1.0 / closeness[s_index];
-                betweenness[s_index] /= isDirected ? (N - 1) * (N - 2) : (N - 1) * (N - 2) / 2;
-            }
-            row.setValue(eccentricityCol, eccentricity[s_index]);
-            row.setValue(closenessCol, closeness[s_index]);
-            row.setValue(betweenessCol, betweenness[s_index]);
+            s.setAttribute(ECCENTRICITY, nodeEccentricity[s_index]);
+            s.setAttribute(CLOSENESS, nodeCloseness[s_index]);
+            s.setAttribute(BETWEENNESS, nodeBetweenness[s_index]);
         }
-        hgraph.readUnlock();
     }
 
     public void setNormalized(boolean isNormalized) {
@@ -330,6 +409,7 @@ public class GraphDistance implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public String getReport() {
         String htmlIMG1 = "";
         String htmlIMG2 = "";
@@ -364,9 +444,10 @@ public class GraphDistance implements Statistics, LongTask {
     }
 
     /**
-     * 
+     *
      * @return
      */
+    @Override
     public boolean cancel() {
         this.isCanceled = true;
         return true;
@@ -376,6 +457,7 @@ public class GraphDistance implements Statistics, LongTask {
      *
      * @param progressTicket
      */
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
         this.progress = progressTicket;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/Hits.java

@@ -1,63 +1,60 @@
 /*
-Copyright 2008-2011 Gephi
-Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2011 Gephi
+ Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s):
+ Contributor(s):
 
-Portions Copyrighted 2011 Gephi Consortium.
+ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics.plugin;
 
 import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeRow;
-import org.gephi.data.attributes.api.AttributeType;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
+import org.gephi.graph.api.DirectedGraph;
 import org.gephi.graph.api.Edge;
 import org.gephi.graph.api.EdgeIterable;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphController;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalDirectedGraph;
-import org.gephi.graph.api.HierarchicalGraph;
-import org.gephi.graph.api.HierarchicalUndirectedGraph;
 import org.gephi.graph.api.Node;
+import org.gephi.graph.api.NodeIterable;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.utils.longtask.spi.LongTask;
 import org.gephi.utils.progress.Progress;
@@ -70,8 +67,8 @@ import org.jfree.data.xy.XYSeriesCollection;
 import org.openide.util.Lookup;
 
 /**
- * Ref: Jon M. Kleinberg, Authoritative Sources in a Hyperlinked Environment,
- * in Journal of the ACM 46 (5): 604–632 (1999)
+ * Ref: Jon M. Kleinberg, Authoritative Sources in a Hyperlinked Environment, in
+ * Journal of the ACM 46 (5): 604–632 (1999)
  *
  * @author pjmcswee
  */
@@ -85,14 +82,11 @@ public class Hits implements Statistics, LongTask {
     private double[] hubs;
     private boolean useUndirected;
     private double epsilon = 0.0001;
-    private LinkedList<Node> hub_list;
-    private LinkedList<Node> auth_list;
-    private HashMap<Node, Integer> indicies;
 
     public Hits() {
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            useUndirected = graphController.getModel().isUndirected();
+        if (graphController != null && graphController.getGraphModel() != null) {
+            useUndirected = graphController.getGraphModel().isUndirected();
         }
     }
 
@@ -101,173 +95,194 @@ public class Hits implements Statistics, LongTask {
     }
 
     /**
-     * 
+     *
      * @return
      */
     public boolean getUndirected() {
         return useUndirected;
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalGraph graph = null;
+        Graph graph = null;
         if (useUndirected) {
-            graph = graphModel.getHierarchicalUndirectedGraphVisible();
+            graph = graphModel.getUndirectedGraphVisible();
         } else {
-            graph = graphModel.getHierarchicalDirectedGraphVisible();
+            graph = graphModel.getDirectedGraphVisible();
         }
         execute(graph, attributeModel);
     }
 
-    public void execute(HierarchicalGraph hgraph, AttributeModel attributeModel) {
+    public void execute(Graph hgraph, AttributeModel attributeModel) {
+
+        initializeAttributeColunms(attributeModel);
+
         hgraph.readLock();
 
         int N = hgraph.getNodeCount();
         authority = new double[N];
         hubs = new double[N];
+
+        Map<Node, Integer> indicies = createIndiciesMap(hgraph);
+
+        calculateHits(hgraph, hubs, authority, indicies, !useUndirected, epsilon);
+
+        saveCalculatedValues(hgraph, authority, hubs);
+
+        hgraph.readUnlockAll();
+    }
+
+    public void calculateHits(Graph hgraph, double[] hubValues, double[] authorityValues, Map<Node, Integer> indicies, boolean isDirected, double eps) {
+
+        int N = hgraph.getNodeCount();
+
         double[] temp_authority = new double[N];
         double[] temp_hubs = new double[N];
 
-        hub_list = new LinkedList<Node>();
-        auth_list = new LinkedList<Node>();
-
+        initializeStartValues(hubValues, authorityValues);
+        
         Progress.start(progress);
 
-        indicies = new HashMap<Node, Integer>();
-        int index = 0;
-        for (Node node : hgraph.getNodes()) {
-            indicies.put(node, new Integer(index));
-            index++;
-
-            if (!useUndirected) {
-                if (((HierarchicalDirectedGraph) hgraph).getTotalOutDegree(node) > 0) {
-                    hub_list.add(node);
-                }
-                if (((HierarchicalDirectedGraph) hgraph).getTotalInDegree(node) > 0) {
-                    auth_list.add(node);
-                }
-            } else {
-                if (((HierarchicalUndirectedGraph) hgraph).getTotalDegree(node) > 0) {
-                    hub_list.add(node);
-                    auth_list.add(node);
-                }
-            }
-        }
-
-
-        for (Node node : hub_list) {
-            int n_index = indicies.get(node);
-            hubs[n_index] = 1.0f;
-        }
-        for (Node node : auth_list) {
-            int n_index = indicies.get(node);
-            authority[n_index] = 1.0f;
-        }
-
         while (true) {
 
             boolean done = true;
-            double auth_sum = 0;
-            for (Node node : auth_list) {
 
-                int n_index = indicies.get(node);
-                temp_authority[n_index] = authority[n_index];
-                EdgeIterable edge_iter;
-                if (!useUndirected) {
-                    edge_iter = ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(node);
-                } else {
-                    edge_iter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(node);
-                }
-                for (Edge edge : edge_iter) {
-                    Node target = hgraph.getOpposite(node, edge);
-                    int target_index = indicies.get(target);
-                    temp_authority[n_index] += hubs[target_index];
-                }
+            updateAutorithy(hgraph, temp_authority, hubValues, isDirected, indicies);
+            updateHub(hgraph, temp_hubs, temp_authority, isDirected, indicies);
 
-                auth_sum += temp_authority[n_index];
-                if (isCanceled) {
-                    break;
-                }
+            done = checkDiff(authorityValues, temp_authority, eps) && checkDiff(hubValues, temp_hubs, eps);
 
-            }
+            System.arraycopy(temp_authority, 0, authorityValues, 0, N);
+            System.arraycopy(temp_hubs, 0, hubValues, 0, N);
 
-            double hub_sum = 0;
-            for (Node node : hub_list) {
-
-                int n_index = indicies.get(node);
-                temp_hubs[n_index] = hubs[n_index];
-                EdgeIterable edge_iter;
-                if (!useUndirected) {
-                    edge_iter = ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(node);
-                } else {
-                    edge_iter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(node);
-                }
-                for (Edge edge : edge_iter) {
-                    Node target = hgraph.getOpposite(node, edge);
-                    int target_index = indicies.get(target);
-                    temp_hubs[n_index] += authority[target_index];
-                }
-                hub_sum += temp_hubs[n_index];
-                if (isCanceled) {
-                    break;
-                }
-            }
-
-            for (Node node : auth_list) {
-                int n_index = indicies.get(node);
-                temp_authority[n_index] /= auth_sum;
-                if (((temp_authority[n_index] - authority[n_index]) / authority[n_index]) >= epsilon) {
-                    done = false;
-                }
-            }
-            for (Node node : hub_list) {
-                int n_index = indicies.get(node);
-                temp_hubs[n_index] /= hub_sum;
-                if (((temp_hubs[n_index] - hubs[n_index]) / hubs[n_index]) >= epsilon) {
-                    done = false;
-                }
-            }
-
-
-            authority = temp_authority;
-            hubs = temp_hubs;
-            temp_authority = new double[N];
-            temp_hubs = new double[N];
+//            temp_authority = new double[N];
+//            temp_hubs = new double[N]
 
             if ((done) || (isCanceled)) {
                 break;
             }
         }
+    }
 
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn authorityCol = nodeTable.getColumn(AUTHORITY);
-        AttributeColumn hubsCol = nodeTable.getColumn(HUB);
-        if (authorityCol == null) {
-            authorityCol = nodeTable.addColumn(AUTHORITY, "Authority", AttributeType.FLOAT, AttributeOrigin.COMPUTED, new Float(0));
-        }
-        if (hubsCol == null) {
-            hubsCol = nodeTable.addColumn(HUB, "Hub", AttributeType.FLOAT, AttributeOrigin.COMPUTED, new Float(0));
-        }
+    private void initializeAttributeColunms(AttributeModel attributeModel) {
+        Table nodeTable = attributeModel.getNodeTable();
 
+        if (!nodeTable.hasColumn(AUTHORITY)) {
+            nodeTable.addColumn(AUTHORITY, "Authority", Float.class, new Float(0));
+        }
+        if (!nodeTable.hasColumn(HUB)) {
+            nodeTable.addColumn(HUB, "Hub", Float.class, new Float(0));
+        }
+    }
+
+    private void initializeStartValues(double[] hubValues, double[] authorityValues) {
+        for (int i = 0; i < authorityValues.length; i++) {
+            authorityValues[i] = 1.0;
+            hubValues[i] = 1.0;
+        }
+    }
+
+    void updateAutorithy(Graph hgraph, double[] newValues, double[] hubValues, boolean isDirected, Map<Node, Integer> indicies) {
+        double norm = 0;
+        int j = 0;
+        for (Node node : hgraph.getNodes()) {
+            double auth = 0;
+            EdgeIterable edge_iter;
+            if (isDirected) {
+                edge_iter = ((DirectedGraph) hgraph).getInEdges(node);
+            } else {
+                edge_iter = hgraph.getEdges(node);
+            }
+            for (Edge edge : edge_iter) {
+                Node target = hgraph.getOpposite(node, edge);
+                auth += hubValues[indicies.get(target)];
+            }
+            if (auth > 0) {
+                newValues[j] = auth;
+            }
+            norm += newValues[j++];
+            if (isCanceled) {
+                return;
+            }
+        }
+//        norm = Math.sqrt(norm);
+        if (norm > 0) {
+            for (int i = 0; i < newValues.length; i++) {
+                newValues[i] = newValues[i] / norm;
+            }
+        }
+    }
+
+    void updateHub(Graph hgraph, double[] newValues, double[] authValues, boolean isDirected, Map<Node, Integer> indicies) {
+        double norm = 0;
+        int j = 0;
+        for (Node node : hgraph.getNodes()) {
+            double hub = 0;
+            EdgeIterable edge_iter;
+            if (isDirected) {
+                edge_iter = ((DirectedGraph) hgraph).getOutEdges(node);
+            } else {
+                edge_iter = hgraph.getEdges(node);
+            }
+            for (Edge edge : edge_iter) {
+                Node target = hgraph.getOpposite(node, edge);
+                hub += authValues[indicies.get(target)];
+            }
+            if(hub > 0) {
+                newValues[j] = hub;
+            }
+            norm += newValues[j++];
+            if (isCanceled) {
+                return;
+            }
+        }
+        if (norm > 0) {
+            for (int i = 0; i < newValues.length; i++) {
+                newValues[i] = newValues[i] / norm;
+            }
+        }
+    }
+
+    private boolean checkDiff(double[] oldValues, double[] newValues, double epsilon) {
+
+        for (int i = 0; i < oldValues.length; i++) {
+            if (oldValues[i] > 0 && ((newValues[i] - oldValues[i]) / oldValues[i]) >= epsilon) {
+                return false;
+            }
+        }
+        return true;
+    }
+
+    private void saveCalculatedValues(Graph hgraph, double[] nodeAuthority, double[] nodeHubs) {
+        int i = 0;
         for (Node s : hgraph.getNodes()) {
-            int s_index = indicies.get(s);
-            AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
-            row.setValue(authorityCol, (float) authority[s_index]);
-            row.setValue(hubsCol, (float) hubs[s_index]);
-        }
+            int s_index = i++;
 
-        hgraph.readUnlockAll();
+            s.setAttribute(AUTHORITY, (float) nodeAuthority[s_index]);
+            s.setAttribute(HUB, (float) nodeHubs[s_index]);
+        }
+    }
+
+    public HashMap<Node, Integer> createIndiciesMap(Graph hgraph) {
+        HashMap<Node, Integer> newIndicies = new HashMap<Node, Integer>();
+        int index = 0;
+        for (Node s : hgraph.getNodes()) {
+            newIndicies.put(s, index);
+            index++;
+        }
+        return newIndicies;
     }
 
     /**
      *
      * @return
      */
+    @Override
     public String getReport() {
         //distribution of hub values
         Map<Double, Integer> distHubs = new HashMap<Double, Integer>();
-        for (Node node : hub_list) {
-            int n_index = indicies.get(node);
-            Double d = hubs[n_index];
+        for (int i = 0; i < hubs.length; i++) {
+            Double d = hubs[i];
             if (distHubs.containsKey(d)) {
                 Integer v = distHubs.get(d);
                 distHubs.put(d, v + 1);
@@ -278,9 +293,8 @@ public class Hits implements Statistics, LongTask {
 
         //distribution of authority values
         Map<Double, Integer> distAuthorities = new HashMap<Double, Integer>();
-        for (Node node : auth_list) {
-            int n_index = indicies.get(node);
-            Double d = authority[n_index];
+        for (int i = 0; i < authority.length; i++) {
+            Double d = authority[i];
             if (distAuthorities.containsKey(d)) {
                 Integer v = distAuthorities.get(d);
                 distAuthorities.put(d, v + 1);
@@ -329,7 +343,6 @@ public class Hits implements Statistics, LongTask {
         ChartUtils.scaleChart(chart2, dAuthsSeries, true);
         String imageFile2 = ChartUtils.renderChart(chart2, "authorities.png");
 
-
         String report = "<HTML> <BODY> <h1> HITS Metric Report </h1>"
                 + "<hr>"
                 + "<br />"
@@ -347,6 +360,7 @@ public class Hits implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public boolean cancel() {
         isCanceled = true;
         return true;
@@ -356,6 +370,7 @@ public class Hits implements Statistics, LongTask {
      *
      * @param progressTicket
      */
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
         progress = progressTicket;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/Modularity.java

@@ -1,52 +1,54 @@
 /*
-Copyright 2008-2011 Gephi
-Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2011 Gephi
+ Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s): Thomas Aynaud <taynaud@gmail.com>
+ Contributor(s): Thomas Aynaud <taynaud@gmail.com>
 
-Portions Copyrighted 2011 Gephi Consortium.
-*/
+ Portions Copyrighted 2011 Gephi Consortium.
+ */
 package org.gephi.statistics.plugin;
 
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
 import java.util.*;
-import org.gephi.data.attributes.api.*;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalUndirectedGraph;
 import org.gephi.graph.api.Node;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.utils.longtask.spi.LongTask;
@@ -73,7 +75,7 @@ public class Modularity implements Statistics, LongTask {
     private boolean isRandomized = false;
     private boolean useWeight = true;
     private double resolution = 1.;
-    
+
     public void setRandom(boolean isRandomized) {
         this.isRandomized = isRandomized;
     }
@@ -81,15 +83,15 @@ public class Modularity implements Statistics, LongTask {
     public boolean getRandom() {
         return isRandomized;
     }
-    
-     public void setUseWeight(boolean useWeight) {
+
+    public void setUseWeight(boolean useWeight) {
         this.useWeight = useWeight;
     }
 
     public boolean getUseWeight() {
         return useWeight;
     }
-    
+
     public void setResolution(double resolution) {
         this.resolution = resolution;
     }
@@ -98,11 +100,13 @@ public class Modularity implements Statistics, LongTask {
         return resolution;
     }
 
+    @Override
     public boolean cancel() {
         this.isCanceled = true;
         return true;
     }
 
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
         this.progress = progressTicket;
     }
@@ -126,7 +130,7 @@ public class Modularity implements Statistics, LongTask {
         HashMap<Modularity.Community, Integer>[] nodeConnectionsCount;
         HashMap<Node, Integer> map;
         Community[] nodeCommunities;
-        HierarchicalUndirectedGraph graph;
+        Graph graph;
         double[] weights;
         double graphWeightSum;
         LinkedList<ModEdge>[] topology;
@@ -134,7 +138,7 @@ public class Modularity implements Statistics, LongTask {
         int N;
         HashMap<Integer, Community> invMap;
 
-        CommunityStructure(HierarchicalUndirectedGraph hgraph) {
+        CommunityStructure(Graph hgraph) {
             this.graph = hgraph;
             N = hgraph.getNodeCount();
             invMap = new HashMap<Integer, Community>();
@@ -156,12 +160,12 @@ public class Modularity implements Statistics, LongTask {
                 Community hidden = new Community(structure);
                 hidden.nodes.add(index);
                 invMap.put(index, hidden);
-                communities.add(nodeCommunities[index]);               
+                communities.add(nodeCommunities[index]);
                 index++;
                 if (isCanceled) {
                     return;
                 }
-            } 
+            }
 
             for (Node node : hgraph.getNodes()) {
                 int node_index = map.get(node);
@@ -173,10 +177,10 @@ public class Modularity implements Statistics, LongTask {
                     }
                     int neighbor_index = map.get(neighbor);
                     float weight = 1;
-                    if(useWeight) {
-                        weight = hgraph.getEdge(node, neighbor).getWeight();
-                    } 
-                      
+                    if (useWeight) {
+                        weight = (float) hgraph.getEdge(node, neighbor).getWeight();
+                    }
+
                     weights[node_index] += weight;
                     Modularity.ModEdge me = new ModEdge(node_index, neighbor_index, weight);
                     topology[node_index].add(me);
@@ -221,9 +225,6 @@ public class Modularity implements Statistics, LongTask {
                     nodeConnectionsCount[neighbor].put(to, neighCountEdgesTo + 1);
                 }
 
-
-
-
                 ///////////////////
                 Modularity.Community adjCom = nodeCommunities[neighbor];
                 Float wEdgesto = adjCom.connectionsWeight.get(to);
@@ -232,7 +233,7 @@ public class Modularity implements Statistics, LongTask {
                 } else {
                     adjCom.connectionsWeight.put(to, wEdgesto + e.weight);
                 }
-                
+
                 Integer cEdgesto = adjCom.connectionsCount.get(to);
                 if (cEdgesto == null) {
                     adjCom.connectionsCount.put(to, 1);
@@ -246,7 +247,7 @@ public class Modularity implements Statistics, LongTask {
                 } else {
                     nodeConnectionsWeight[node].put(adjCom, nodeEdgesTo + e.weight);
                 }
-                
+
                 Integer nodeCountEdgesTo = nodeConnectionsCount[node].get(adjCom);
                 if (nodeCountEdgesTo == null) {
                     nodeConnectionsCount[node].put(adjCom, 1);
@@ -261,21 +262,20 @@ public class Modularity implements Statistics, LongTask {
                     } else {
                         to.connectionsWeight.put(adjCom, comEdgesto + e.weight);
                     }
-                    
+
                     Integer comCountEdgesto = to.connectionsCount.get(adjCom);
                     if (comCountEdgesto == null) {
                         to.connectionsCount.put(adjCom, 1);
                     } else {
                         to.connectionsCount.put(adjCom, comCountEdgesto + 1);
                     }
-                    
-                    
+
                 }
             }
         }
 
         private void removeNodeFrom(int node, Community from) {
-                       
+
             Community community = nodeCommunities[node];
             for (ModEdge e : topology[node]) {
                 int neighbor = e.target;
@@ -304,9 +304,7 @@ public class Modularity implements Statistics, LongTask {
                     adjCom.connectionsWeight.put(community, oEdgesto - e.weight);
                     adjCom.connectionsCount.put(community, oCountEdgesto - 1);
                 }
-                
 
-                
                 if (node == neighbor) {
                     continue;
                 }
@@ -333,7 +331,6 @@ public class Modularity implements Statistics, LongTask {
                     nodeConnectionsCount[node].put(adjCom, nodeCountEgesTo - 1);
                 }
 
-
             }
             from.remove(new Integer(node));
         }
@@ -367,13 +364,14 @@ public class Modularity implements Statistics, LongTask {
                     hidden.nodes.addAll(oldHidden.nodes);
                 }
                 newInvMap.put(index, hidden);
-                for(Modularity.Community adjCom : iter) {
+                for (Modularity.Community adjCom : iter) {
                     int target = communities.indexOf(adjCom);
                     float weight = com.connectionsWeight.get(adjCom);
-                    if(target == index)
-                        weightSum += 2.*weight;
-                    else
+                    if (target == index) {
+                        weightSum += 2. * weight;
+                    } else {
                         weightSum += weight;
+                    }
                     ModEdge e = new ModEdge(index, target, weight);
                     newTopology[index].add(e);
                 }
@@ -403,6 +401,7 @@ public class Modularity implements Statistics, LongTask {
     }
 
     class Community {
+
         double weightSum;
         CommunityStructure structure;
         LinkedList<Integer> nodes;
@@ -449,22 +448,44 @@ public class Modularity implements Statistics, LongTask {
         }
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalUndirectedGraph hgraph = graphModel.getHierarchicalUndirectedGraphVisible();
+        Graph hgraph = graphModel.getUndirectedGraphVisible();
         execute(hgraph, attributeModel);
     }
 
-    public void execute(HierarchicalUndirectedGraph hgraph, AttributeModel attributeModel) {
+    public void execute(Graph hgraph, AttributeModel attributeModel) {
+        isCanceled = false;
+
+        hgraph.readLock();
+
+        structure = new Modularity.CommunityStructure(hgraph);
+        int[] comStructure = new int[hgraph.getNodeCount()];
+
+        HashMap<String, Double> computedModularityMetrics = computeModularity(hgraph, structure, comStructure, resolution, isRandomized, useWeight);
+
+        modularity = computedModularityMetrics.get("modularity");
+        modularityResolution = computedModularityMetrics.get("modularityResolution");
+
+        saveValues(comStructure, hgraph, attributeModel, structure);
+
+        hgraph.readUnlock();
+    }
+
+    protected HashMap<String, Double> computeModularity(Graph hgraph, CommunityStructure theStructure, int[] comStructure,
+            double currentResolution, boolean randomized, boolean weighted) {
         isCanceled = false;
         Progress.start(progress);
         Random rand = new Random();
-        hgraph.readLock();
-        structure = new Modularity.CommunityStructure(hgraph);
-        double totalWeight = structure.graphWeightSum;
-        double[] nodeDegrees = structure.weights.clone();
+
+        double totalWeight = theStructure.graphWeightSum;
+        double[] nodeDegrees = theStructure.weights.clone();
+
+        HashMap<String, Double> results = new HashMap<String, Double>();
+
         if (isCanceled) {
             hgraph.readUnlockAll();
-            return;
+            return results;
         }
         boolean someChange = true;
         while (someChange) {
@@ -473,92 +494,105 @@ public class Modularity implements Statistics, LongTask {
             while (localChange) {
                 localChange = false;
                 int start = 0;
-                if (isRandomized) {
-                    start = Math.abs(rand.nextInt()) % structure.N;
+                if (randomized) {
+                    start = Math.abs(rand.nextInt()) % theStructure.N;
                 }
                 int step = 0;
-                for (int i = start; step < structure.N; i = (i + 1) % structure.N) {
+                for (int i = start; step < theStructure.N; i = (i + 1) % theStructure.N) {
                     step++;
-                    double best = 0.;
-                    Community bestCommunity = null;
-                    Community nodecom = structure.nodeCommunities[i];
-                    Set<Community> iter = structure.nodeConnectionsWeight[i].keySet();
-                    for(Community com : iter) {
-                        double qValue = q(i, com);
-                        if (qValue > best) {
-                            best = qValue;
-                            bestCommunity = com;
-                        } 
-                    }
-                    if ((structure.nodeCommunities[i] != bestCommunity) && (bestCommunity != null)) {
-                        structure.moveNodeTo(i, bestCommunity);
+                    Community bestCommunity = updateBestCommunity(theStructure, i, currentResolution);
+                    if ((theStructure.nodeCommunities[i] != bestCommunity) && (bestCommunity != null)) {
+                        theStructure.moveNodeTo(i, bestCommunity);
                         localChange = true;
                     }
                     if (isCanceled) {
                         hgraph.readUnlockAll();
-                        return;
+                        return results;
                     }
                 }
                 someChange = localChange || someChange;
                 if (isCanceled) {
                     hgraph.readUnlockAll();
-                    return;
+                    return results;
                 }
             }
 
             if (someChange) {
-                structure.zoomOut();
+                theStructure.zoomOut();
             }
         }
 
-        int[] comStructure = new int[hgraph.getNodeCount()];
+        fillComStructure(hgraph, theStructure, comStructure);
+        double[] degreeCount = fillDegreeCount(hgraph, theStructure, comStructure, nodeDegrees, weighted);
+
+        double computedModularity = finalQ(comStructure, degreeCount, hgraph, theStructure, totalWeight, 1., weighted);
+        double computedModularityResolution = finalQ(comStructure, degreeCount, hgraph, theStructure, totalWeight, currentResolution, weighted);
+
+        results.put("modularity", computedModularity);
+        results.put("modularityResolution", computedModularityResolution);
+
+        return results;
+    }
+
+    Community updateBestCommunity(CommunityStructure theStructure, int i, double currentResolution) {
+        double best = 0.;
+        Community bestCommunity = null;
+        Set<Community> iter = theStructure.nodeConnectionsWeight[i].keySet();
+        for (Community com : iter) {
+            double qValue = q(i, com, theStructure, currentResolution);
+            if (qValue > best) {
+                best = qValue;
+                bestCommunity = com;
+            }
+        }
+        return bestCommunity;
+    }
+
+    int[] fillComStructure(Graph hgraph, CommunityStructure theStructure, int[] comStructure) {
+//        int[] comStructure = new int[hgraph.getNodeCount()];
         int count = 0;
-        double[] degreeCount = new double[structure.communities.size()];
-        for (Community com : structure.communities) {
+
+        for (Community com : theStructure.communities) {
             for (Integer node : com.nodes) {
-                Community hidden = structure.invMap.get(node);
+                Community hidden = theStructure.invMap.get(node);
                 for (Integer nodeInt : hidden.nodes) {
                     comStructure[nodeInt] = count;
                 }
             }
             count++;
         }
-        for (Node node : hgraph.getNodes()) {
-            int index = structure.map.get(node);
-            if(useWeight) {
-                degreeCount[comStructure[index]] += nodeDegrees[index];
-            } else {                
-                degreeCount[comStructure[index]] += hgraph.getTotalDegree(node);
-            }
-            
-        }
-        
-        modularity = finalQ(comStructure, degreeCount, hgraph, attributeModel, totalWeight, 1.);
-        modularityResolution = finalQ(comStructure, degreeCount, hgraph, attributeModel, totalWeight, resolution);
-        
-        hgraph.readUnlock();
+        return comStructure;
     }
 
-    private double finalQ(int[] struct, double[] degrees, HierarchicalUndirectedGraph hgraph, AttributeModel attributeModel, double totalWeight, double usedResolution) {
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn modCol = nodeTable.getColumn(MODULARITY_CLASS);
-        if (modCol == null) {
-            modCol = nodeTable.addColumn(MODULARITY_CLASS, "Modularity Class", AttributeType.INT, AttributeOrigin.COMPUTED, new Integer(0));
+    double[] fillDegreeCount(Graph hgraph, CommunityStructure theStructure, int[] comStructure, double[] nodeDegrees, boolean weighted) {
+        double[] degreeCount = new double[theStructure.communities.size()];
+
+        for (Node node : hgraph.getNodes()) {
+            int index = theStructure.map.get(node);
+            if (weighted) {
+                degreeCount[comStructure[index]] += nodeDegrees[index];
+            } else {
+                degreeCount[comStructure[index]] += hgraph.getDegree(node);
+            }
+
         }
+        return degreeCount;
+    }
+
+    private double finalQ(int[] struct, double[] degrees, Graph hgraph,
+            CommunityStructure theStructure, double totalWeight, double usedResolution, boolean weighted) {
 
         double res = 0;
         double[] internal = new double[degrees.length];
         for (Node n : hgraph.getNodes()) {
-            int n_index = structure.map.get(n);
-            AttributeRow row = (AttributeRow) n.getNodeData().getAttributes();
-            row.setValue(modCol, struct[n_index]);
+            int n_index = theStructure.map.get(n);
             for (Node neighbor : hgraph.getNeighbors(n)) {
                 if (n == neighbor) {
                     continue;
                 }
-                int neigh_index = structure.map.get(neighbor);
+                int neigh_index = theStructure.map.get(neighbor);
                 if (struct[neigh_index] == struct[n_index]) {
-                    if(useWeight) {
+                    if (weighted) {
                         internal[struct[neigh_index]] += hgraph.getEdge(n, neighbor).getWeight();
                     } else {
                         internal[struct[neigh_index]]++;
@@ -573,21 +607,34 @@ public class Modularity implements Statistics, LongTask {
         return res;
     }
 
+    private void saveValues(int[] struct, Graph hgraph, AttributeModel attributeModel, CommunityStructure theStructure) {
+        Table nodeTable = attributeModel.getNodeTable();
+        Column modCol = nodeTable.getColumn(MODULARITY_CLASS);
+        if (modCol == null) {
+            modCol = nodeTable.addColumn(MODULARITY_CLASS, "Modularity Class", Integer.class, new Integer(0));
+        }
+        for (Node n : hgraph.getNodes()) {
+            int n_index = theStructure.map.get(n);;
+            n.setAttribute(modCol, struct[n_index]);
+        }
+    }
+
     public double getModularity() {
         return modularity;
     }
 
+    @Override
     public String getReport() {
         //Distribution series
         Map<Integer, Integer> sizeDist = new HashMap<Integer, Integer>();
-        for(Node n : structure.graph.getNodes()) {
-            Integer v = (Integer) n.getNodeData().getAttributes().getValue(MODULARITY_CLASS);
-            if(!sizeDist.containsKey(v)) {
+        for (Node n : structure.graph.getNodes()) {
+            Integer v = (Integer) n.getAttribute(MODULARITY_CLASS);
+            if (!sizeDist.containsKey(v)) {
                 sizeDist.put(v, 0);
             }
             sizeDist.put(v, sizeDist.get(v) + 1);
         }
-        
+
         XYSeries dSeries = ChartUtils.createXYSeries(sizeDist, "Size Distribution");
 
         XYSeriesCollection dataset1 = new XYSeriesCollection();
@@ -607,20 +654,19 @@ public class Modularity implements Statistics, LongTask {
         ChartUtils.scaleChart(chart, dSeries, false);
         String imageFile = ChartUtils.renderChart(chart, "communities-size-distribution.png");
 
-        
         NumberFormat f = new DecimalFormat("#0.000");
 
         String report = "<HTML> <BODY> <h1>Modularity Report </h1> "
                 + "<hr>"
                 + "<h2> Parameters: </h2>"
                 + "Randomize:  " + (isRandomized ? "On" : "Off") + "<br>"
-                + "Use edge weights:  " + (useWeight ? "On" : "Off") + "<br>"                 
-                + "Resolution:  " + (resolution) + "<br>"                 
+                + "Use edge weights:  " + (useWeight ? "On" : "Off") + "<br>"
+                + "Resolution:  " + (resolution) + "<br>"
                 + "<br> <h2> Results: </h2>"
                 + "Modularity: " + f.format(modularity) + "<br>"
                 + "Modularity with resolution: " + f.format(modularityResolution) + "<br>"
                 + "Number of Communities: " + structure.communities.size()
-                + "<br /><br />"+imageFile
+                + "<br /><br />" + imageFile
                 + "<br /><br />" + "<h2> Algorithm: </h2>"
                 + "Vincent D Blondel, Jean-Loup Guillaume, Renaud Lambiotte, Etienne Lefebvre, <i>Fast unfolding of communities in large networks</i>, in Journal of Statistical Mechanics: Theory and Experiment 2008 (10), P1000<br />"
                 + "<br /><br />" + "<h2> Resolution: </h2>"
@@ -630,19 +676,19 @@ public class Modularity implements Statistics, LongTask {
         return report;
     }
 
-    private double q(int node, Community community) {
-        Float edgesToFloat = structure.nodeConnectionsWeight[node].get(community);
+    private double q(int node, Community community, CommunityStructure theStructure, double currentResolution) {
+        Float edgesToFloat = theStructure.nodeConnectionsWeight[node].get(community);
         double edgesTo = 0;
         if (edgesToFloat != null) {
             edgesTo = edgesToFloat.doubleValue();
         }
         double weightSum = community.weightSum;
-        double nodeWeight = structure.weights[node];
-        double qValue = resolution * edgesTo - (nodeWeight * weightSum) / (2.0 * structure.graphWeightSum);
-        if ((structure.nodeCommunities[node] == community) && (structure.nodeCommunities[node].size() > 1)) {
-            qValue = resolution * edgesTo - (nodeWeight * (weightSum - nodeWeight)) / (2.0 * structure.graphWeightSum);
+        double nodeWeight = theStructure.weights[node];
+        double qValue = currentResolution * edgesTo - (nodeWeight * weightSum) / (2.0 * theStructure.graphWeightSum);
+        if ((theStructure.nodeCommunities[node] == community) && (theStructure.nodeCommunities[node].size() > 1)) {
+            qValue = currentResolution * edgesTo - (nodeWeight * (weightSum - nodeWeight)) / (2.0 * theStructure.graphWeightSum);
         }
-        if ((structure.nodeCommunities[node] == community) && (structure.nodeCommunities[node].size() == 1)) {
+        if ((theStructure.nodeCommunities[node] == community) && (theStructure.nodeCommunities[node].size() == 1)) {
             qValue = 0.;
         }
         return qValue;

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/PageRank.java

@@ -1,62 +1,59 @@
 /*
-Copyright 2008-2011 Gephi
-Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2011 Gephi
+ Authors : Patick J. McSweeney <pjmcswee@syr.edu>, Sebastien Heymann <seb@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s):
+ Contributor(s):
 
-Portions Copyrighted 2011 Gephi Consortium.
+ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics.plugin;
 
 import java.util.HashMap;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeRow;
-import org.gephi.data.attributes.api.AttributeType;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
+import org.gephi.graph.api.DirectedGraph;
 import org.gephi.graph.api.Edge;
 import org.gephi.graph.api.EdgeIterable;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphController;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalDirectedGraph;
-import org.gephi.graph.api.HierarchicalGraph;
-import org.gephi.graph.api.HierarchicalUndirectedGraph;
 import org.gephi.graph.api.Node;
+import org.gephi.graph.api.UndirectedGraph;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.utils.longtask.spi.LongTask;
 import org.gephi.utils.progress.Progress;
@@ -69,32 +66,45 @@ import org.jfree.data.xy.XYSeriesCollection;
 import org.openide.util.Lookup;
 
 /**
- * Ref: Sergey Brin, Lawrence Page, The Anatomy of a Large-Scale Hypertextual Web Search Engine, 
- * in Proceedings of the seventh International Conference on the World Wide Web (WWW1998):107-117
+ * Ref: Sergey Brin, Lawrence Page, The Anatomy of a Large-Scale Hypertextual
+ * Web Search Engine, in Proceedings of the seventh International Conference on
+ * the World Wide Web (WWW1998):107-117
  *
  * @author pjmcswee
  */
 public class PageRank implements Statistics, LongTask {
 
     public static final String PAGERANK = "pageranks";
-    /** */
+    /**
+     *
+     */
     private ProgressTicket progress;
-    /** */
+    /**
+     *
+     */
     private boolean isCanceled;
-    /** */
+    /**
+     *
+     */
     private double epsilon = 0.001;
-    /** */
+    /**
+     *
+     */
     private double probability = 0.85;
     private boolean useEdgeWeight = false;
-    /** */
+    /**
+     *
+     */
     private double[] pageranks;
-    /** */
+    /**
+     *
+     */
     private boolean isDirected;
 
     public PageRank() {
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            isDirected = graphController.getModel().isDirected();
+        if (graphController != null && graphController.getGraphModel() != null) {
+            isDirected = graphController.getGraphModel().isDirected();
         }
     }
 
@@ -110,43 +120,65 @@ public class PageRank implements Statistics, LongTask {
         return isDirected;
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalGraph graph;
+        Graph graph;
         if (isDirected) {
-            graph = graphModel.getHierarchicalDirectedGraphVisible();
+            graph = graphModel.getDirectedGraphVisible();
         } else {
-            graph = graphModel.getHierarchicalUndirectedGraphVisible();
+            graph = graphModel.getUndirectedGraphVisible();
         }
         execute(graph, attributeModel);
     }
 
-    public void execute(HierarchicalGraph hgraph, AttributeModel attributeModel) {
+    public void execute(Graph hgraph, AttributeModel attributeModel) {
         isCanceled = false;
 
+        Column column = initializeAttributeColunms(attributeModel);
+
         hgraph.readLock();
 
-        int N = hgraph.getNodeCount();
-        pageranks = new double[N];
-        double[] temp = new double[N];
-        HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
-        int index = 0;
+        HashMap<Node, Integer> indicies = createIndiciesMap(hgraph);
 
-        Progress.start(progress);
-        double[] weights = null;
-        if (useEdgeWeight) {
-            weights = new double[N];
+        pageranks = calculatePagerank(hgraph, indicies, isDirected, useEdgeWeight, epsilon, probability);
+
+        saveCalculatedValues(hgraph, column, indicies, pageranks);
+
+        hgraph.readUnlockAll();
+    }
+
+    private Column initializeAttributeColunms(AttributeModel attributeModel) {
+        Table nodeTable = attributeModel.getNodeTable();
+        Column pagerankCol = nodeTable.getColumn(PAGERANK);
+
+        if (pagerankCol == null) {
+            pagerankCol = nodeTable.addColumn(PAGERANK, "PageRank", Double.class, new Double(0));
         }
 
+        return pagerankCol;
+    }
+
+    private void saveCalculatedValues(Graph hgraph, Column attributeColumn, HashMap<Node, Integer> indicies,
+            double[] nodePagrank) {
         for (Node s : hgraph.getNodes()) {
-            indicies.put(s, index);
-            pageranks[index] = 1.0f / N;
-            if (useEdgeWeight) {
+            int s_index = indicies.get(s);
+
+            s.setAttribute(attributeColumn, nodePagrank[s_index]);
+        }
+    }
+
+    private void setInitialValues(Graph hgraph, double[] pagerankValues, double[] weights, boolean directed, boolean useWeights) {
+        int N = hgraph.getNodeCount();
+        int index = 0;
+        for (Node s : hgraph.getNodes()) {
+            pagerankValues[index] = 1.0f / N;
+            if (useWeights) {
                 double sum = 0;
                 EdgeIterable eIter;
-                if (isDirected) {
-                    eIter = ((HierarchicalDirectedGraph) hgraph).getOutEdgesAndMetaOutEdges(s);
+                if (directed) {
+                    eIter = ((DirectedGraph) hgraph).getOutEdges(s);
                 } else {
-                    eIter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(s);
+                    eIter = ((UndirectedGraph) hgraph).getEdges(s);
                 }
                 for (Edge edge : eIter) {
                     sum += edge.getWeight();
@@ -155,96 +187,116 @@ public class PageRank implements Statistics, LongTask {
             }
             index++;
         }
+    }
+
+    private double calculateR(Graph hgraph, double[] pagerankValues, HashMap<Node, Integer> indicies, boolean directed, double prob) {
+        int N = hgraph.getNodeCount();
+        double r = 0;
+        for (Node s : hgraph.getNodes()) {
+            int s_index = indicies.get(s);
+            boolean out;
+            if (directed) {
+                out = ((DirectedGraph) hgraph).getOutDegree(s) > 0;
+            } else {
+                out = hgraph.getDegree(s) > 0;
+            }
+
+            if (out) {
+                r += (1.0 - prob) * (pagerankValues[s_index] / N);
+            } else {
+                r += (pagerankValues[s_index] / N);
+            }
+            if (isCanceled) {
+                hgraph.readUnlockAll();
+                return r;
+            }
+        }
+        return r;
+    }
+
+    private double updateValueForNode(Graph hgraph, Node s, double[] pagerankValues, double[] weights,
+            HashMap<Node, Integer> indicies, boolean directed, boolean useWeights, double r, double prob) {
+        double res = r;
+        EdgeIterable eIter;
+        if (directed) {
+            eIter = ((DirectedGraph) hgraph).getInEdges(s);
+        } else {
+            eIter = hgraph.getEdges(s);
+        }
+
+        for (Edge edge : eIter) {
+            Node neighbor = hgraph.getOpposite(s, edge);
+            int neigh_index = indicies.get(neighbor);
+            int normalize;
+            if (directed) {
+                normalize = ((DirectedGraph) hgraph).getOutDegree(neighbor);
+            } else {
+                normalize = hgraph.getDegree(neighbor);
+            }
+            if (useWeights) {
+                double weight = edge.getWeight() / weights[neigh_index];
+                res += prob * pagerankValues[neigh_index] * weight;
+            } else {
+                res += prob * (pagerankValues[neigh_index] / normalize);
+            }
+        }
+        return res;
+    }
+
+    double[] calculatePagerank(Graph hgraph, HashMap<Node, Integer> indicies,
+            boolean directed, boolean useWeights, double eps, double prob) {
+        int N = hgraph.getNodeCount();
+        double[] pagerankValues = new double[N];
+        double[] temp = new double[N];
+
+        Progress.start(progress);
+        double[] weights = new double[N];
+
+        setInitialValues(hgraph, pagerankValues, weights, directed, useWeights);
 
         while (true) {
-            double r = 0;
-            for (Node s : hgraph.getNodes()) {
-                int s_index = indicies.get(s);
-                boolean out;
-                if (isDirected) {
-                    out = ((HierarchicalDirectedGraph) hgraph).getTotalOutDegree(s) > 0;
-                } else {
-                    out = hgraph.getTotalDegree(s) > 0;
-                }
-
-                if (out) {
-                    r += (1.0 - probability) * (pageranks[s_index] / N);
-                } else {
-                    r += (pageranks[s_index] / N);
-                }
-                if (isCanceled) {
-                    hgraph.readUnlockAll();
-                    return;
-                }
-            }
+            double r = calculateR(hgraph, pagerankValues, indicies, directed, prob);
 
             boolean done = true;
             for (Node s : hgraph.getNodes()) {
                 int s_index = indicies.get(s);
-                temp[s_index] = r;
+                temp[s_index] = updateValueForNode(hgraph, s, pagerankValues, weights, indicies, directed, useWeights, r, prob);
 
-                EdgeIterable eIter;
-                if (isDirected) {
-                    eIter = ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(s);
-                } else {
-                    eIter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(s);
-                }
-
-                for (Edge edge : eIter) {
-                    Node neighbor = hgraph.getOpposite(s, edge);
-                    int neigh_index = indicies.get(neighbor);
-                    int normalize;
-                    if (isDirected) {
-                        normalize = ((HierarchicalDirectedGraph) hgraph).getTotalOutDegree(neighbor);
-                    } else {
-                        normalize = ((HierarchicalUndirectedGraph) hgraph).getTotalDegree(neighbor);
-                    }
-                    if (useEdgeWeight) {
-                        double weight = edge.getWeight() / weights[neigh_index];
-                        temp[s_index] += probability * pageranks[neigh_index] * weight;
-                    } else {
-                        temp[s_index] += probability * (pageranks[neigh_index] / normalize);
-                    }
-
-                }
-
-                if ((temp[s_index] - pageranks[s_index]) / pageranks[s_index] >= epsilon) {
+                if ((temp[s_index] - pagerankValues[s_index]) / pagerankValues[s_index] >= eps) {
                     done = false;
                 }
 
                 if (isCanceled) {
                     hgraph.readUnlockAll();
-                    return;
+                    return pagerankValues;
                 }
 
             }
-            pageranks = temp;
+            pagerankValues = temp;
             temp = new double[N];
             if ((done) || (isCanceled)) {
                 break;
             }
 
         }
+        return pagerankValues;
+    }
 
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn pangeRanksCol = nodeTable.getColumn(PAGERANK);
-        if (pangeRanksCol == null) {
-            pangeRanksCol = nodeTable.addColumn(PAGERANK, "PageRank", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
-        }
-
+    public HashMap<Node, Integer> createIndiciesMap(Graph hgraph) {
+        HashMap<Node, Integer> newIndicies = new HashMap<Node, Integer>();
+        int index = 0;
         for (Node s : hgraph.getNodes()) {
-            int s_index = indicies.get(s);
-            AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
-            row.setValue(pangeRanksCol, pageranks[s_index]);
+            newIndicies.put(s, index);
+            index++;
         }
-
-        hgraph.readUnlockAll();
+        return newIndicies;
     }
 
     /**
      *
      * @return
      */
+    @Override
     public String getReport() {
         //distribution of values
         Map<Double, Integer> dist = new HashMap<Double, Integer>();
@@ -277,7 +329,7 @@ public class PageRank implements Statistics, LongTask {
         ChartUtils.decorateChart(chart);
         ChartUtils.scaleChart(chart, dSeries, true);
         String imageFile = ChartUtils.renderChart(chart, "pageranks.png");
-        
+
         String report = "<HTML> <BODY> <h1>PageRank Report </h1> "
                 + "<hr> <br />"
                 + "<h2> Parameters: </h2>"
@@ -297,6 +349,7 @@ public class PageRank implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public boolean cancel() {
         isCanceled = true;
         return true;
@@ -306,6 +359,7 @@ public class PageRank implements Statistics, LongTask {
      *
      * @param progressTicket
      */
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
         progress = progressTicket;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/WeightedDegree.java

@@ -46,17 +46,12 @@ import java.text.NumberFormat;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeRow;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeType;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Table;
 import org.gephi.graph.api.DirectedGraph;
 import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalDirectedGraph;
-import org.gephi.graph.api.HierarchicalGraph;
 import org.gephi.graph.api.Node;
 import org.gephi.statistics.spi.Statistics;
 import org.gephi.utils.longtask.spi.LongTask;
@@ -67,6 +62,7 @@ import org.jfree.chart.JFreeChart;
 import org.jfree.chart.plot.PlotOrientation;
 import org.jfree.data.xy.XYSeries;
 import org.jfree.data.xy.XYSeriesCollection;
+import org.openide.util.NbBundle;
 
 /**
  *
@@ -89,93 +85,123 @@ public class WeightedDegree implements Statistics, LongTask {
         return avgWDegree;
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalGraph graph = graphModel.getHierarchicalGraphVisible();
+        Graph graph = graphModel.getGraphVisible();
         execute(graph, attributeModel);
     }
 
-    public void execute(HierarchicalGraph graph, AttributeModel attributeModel) {
-        isDirected = graph instanceof DirectedGraph;
+    public void execute(Graph graph, AttributeModel attributeModel) {
+        isDirected = graph.isDirected();
         isCanceled = false;
-        degreeDist = new HashMap<Double, Integer>();
-        inDegreeDist = new HashMap<Double, Integer>();
-        outDegreeDist = new HashMap<Double, Integer>();
 
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn degCol = nodeTable.getColumn(WDEGREE);
-        AttributeColumn inCol = nodeTable.getColumn(WINDEGREE);
-        AttributeColumn outCol = nodeTable.getColumn(WOUTDEGREE);
-        if (degCol == null) {
-            degCol = nodeTable.addColumn(WDEGREE, "Weighted Degree", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, 0.0);
-        }
-        if (isDirected) {
-            if (inCol == null) {
-                inCol = nodeTable.addColumn(WINDEGREE, "Weighted In-Degree", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, 0.0);
-            }
-            if (outCol == null) {
-                outCol = nodeTable.addColumn(WOUTDEGREE, "Weighted Out-Degree", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, 0.0);
-            }
-        }
+        initializeDegreeDists();
+        initializeAttributeColunms(attributeModel);
 
         graph.readLock();
 
-        Progress.start(progress, graph.getNodeCount());
-        int i = 0;
-
-        for (Node n : graph.getNodes()) {
-            AttributeRow row = (AttributeRow) n.getNodeData().getAttributes();
-            double totalWeight = 0;
-            if (isDirected) {
-                HierarchicalDirectedGraph hdg = graph.getGraphModel().getHierarchicalDirectedGraph();
-                double totalInWeight = 0;
-                double totalOutWeight = 0;
-                for (Iterator it = graph.getEdgesAndMetaEdges(n).iterator(); it.hasNext();) {
-                    Edge e = (Edge) it.next();
-                    if (e.getSource().getNodeData().equals(n.getNodeData())) {
-                        totalOutWeight += e.getWeight();
-                    }
-                    if (e.getTarget().getNodeData().equals(n.getNodeData())) {
-                        totalInWeight += e.getWeight();
-                    }
-                }
-                totalWeight = totalInWeight + totalOutWeight;
-                row.setValue(inCol, totalInWeight);
-                row.setValue(outCol, totalOutWeight);
-                if (!inDegreeDist.containsKey(totalInWeight)) {
-                    inDegreeDist.put(totalInWeight, 0);
-                }
-                inDegreeDist.put(totalInWeight, inDegreeDist.get(totalInWeight) + 1);
-                if (!outDegreeDist.containsKey(totalOutWeight)) {
-                    outDegreeDist.put(totalOutWeight, 0);
-                }
-                outDegreeDist.put(totalOutWeight, outDegreeDist.get(totalOutWeight) + 1);
-            } else {
-                for (Iterator it = graph.getEdgesAndMetaEdges(n).iterator(); it.hasNext();) {
-                    Edge e = (Edge) it.next();
-                    totalWeight += e.getWeight();
-                }
-            }
-
-            row.setValue(degCol, totalWeight);
-            avgWDegree += totalWeight;
-
-            if (!degreeDist.containsKey(totalWeight)) {
-                degreeDist.put(totalWeight, 0);
-            }
-            degreeDist.put(totalWeight, degreeDist.get(totalWeight) + 1);
-
-            if (isCanceled) {
-                break;
-            }
-            i++;
-            Progress.progress(progress, i);
-        }
-
-        avgWDegree /= (isDirected) ? 2 * graph.getNodeCount() : graph.getNodeCount();
+        avgWDegree = calculateAverageWeightedDegree(graph, isDirected, true);
 
         graph.readUnlockAll();
     }
 
+    public double calculateAverageWeightedDegree(Graph graph, boolean isDirected, boolean updateAttributes) {
+        double averageWeightedDegree = 0;
+
+        DirectedGraph directedGraph = null;
+
+        if (isDirected) {
+            directedGraph = (DirectedGraph) graph;
+        }
+
+        Progress.start(progress, graph.getNodeCount());
+
+        for (Node n : graph.getNodes()) {
+            double totalWeight = 0;
+            if (isDirected) {
+                double totalInWeight = 0;
+                double totalOutWeight = 0;
+                for (Edge e : directedGraph.getEdges(n)) {
+                    if (e.getSource().equals(n)) {
+                        totalOutWeight += e.getWeight();
+                    }
+                    if (e.getTarget().equals(n)) {
+                        totalInWeight += e.getWeight();
+                    }
+                }
+                totalWeight = totalInWeight + totalOutWeight;
+
+                n.setAttribute(WINDEGREE, totalInWeight);
+                n.setAttribute(WOUTDEGREE, totalOutWeight);
+                n.setAttribute(WDEGREE, totalWeight);
+
+                updateDegreeDists(totalInWeight, totalOutWeight, totalWeight);
+            } else {
+                for (Edge e : graph.getEdges(n)) {
+                    totalWeight += e.getWeight();
+                }
+                n.setAttribute(WDEGREE, totalWeight);
+                updateDegreeDists(totalWeight);
+            }
+
+            averageWeightedDegree += totalWeight;
+
+            if (isCanceled) {
+                break;
+            }
+            Progress.progress(progress);
+        }
+
+        averageWeightedDegree /= (isDirected) ? 2 * graph.getNodeCount() : graph.getNodeCount();
+
+        return averageWeightedDegree;
+
+    }
+
+    private void initializeDegreeDists() {
+        degreeDist = new HashMap<Double, Integer>();
+        inDegreeDist = new HashMap<Double, Integer>();
+        outDegreeDist = new HashMap<Double, Integer>();
+    }
+
+    private void initializeAttributeColunms(AttributeModel attributeModel) {
+        Table nodeTable = attributeModel.getNodeTable();
+        if (isDirected) {
+            if (!nodeTable.hasColumn(WINDEGREE)) {
+                nodeTable.addColumn(WINDEGREE, NbBundle.getMessage(WeightedDegree.class, "WeightedDegree.nodecolumn.InDegree"), Double.class, 0.0);
+            }
+            if (!nodeTable.hasColumn(WOUTDEGREE)) {
+                nodeTable.addColumn(WOUTDEGREE, NbBundle.getMessage(WeightedDegree.class, "WeightedDegree.nodecolumn.OutDegree"), Double.class, 0.0);
+            }
+        }
+        if (!nodeTable.hasColumn(WDEGREE)) {
+            nodeTable.addColumn(WDEGREE, NbBundle.getMessage(WeightedDegree.class, "WeightedDegree.nodecolumn.Degree"), Double.class, 0.0);
+        }
+    }
+
+    private void updateDegreeDists(double winDegree, double woutDegree, double wdegree) {
+        if (!inDegreeDist.containsKey(winDegree)) {
+            inDegreeDist.put(winDegree, 0);
+        }
+        inDegreeDist.put(winDegree, inDegreeDist.get(winDegree) + 1);
+        if (!outDegreeDist.containsKey(woutDegree)) {
+            outDegreeDist.put(woutDegree, 0);
+        }
+        outDegreeDist.put(woutDegree, outDegreeDist.get(woutDegree) + 1);
+        if (!degreeDist.containsKey(wdegree)) {
+            degreeDist.put(wdegree, 0);
+        }
+        degreeDist.put(wdegree, degreeDist.get(wdegree) + 1);
+    }
+
+    private void updateDegreeDists(double wdegree) {
+        if (!degreeDist.containsKey(wdegree)) {
+            degreeDist.put(wdegree, 0);
+        }
+        degreeDist.put(wdegree, degreeDist.get(wdegree) + 1);
+    }
+
+    @Override
     public String getReport() {
         String report = "";
 
@@ -282,11 +308,13 @@ public class WeightedDegree implements Statistics, LongTask {
         return report;
     }
 
+    @Override
     public boolean cancel() {
         this.isCanceled = true;
         return true;
     }
 
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
         this.progress = progressTicket;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/ClusteringCoefficientBuilder.java

@@ -38,31 +38,34 @@ made subject to such option by the copyright holder.
 Contributor(s):
 
 Portions Copyrighted 2011 Gephi Consortium.
-*/
-package org.gephi.statistics.plugin.builder;
-
-import org.gephi.statistics.plugin.ClusteringCoefficient;
-import org.gephi.statistics.spi.Statistics;
-import org.gephi.statistics.spi.StatisticsBuilder;
-import org.openide.util.NbBundle;
-import org.openide.util.lookup.ServiceProvider;
-
-/**
- *
- * @author pjmcswee
- */
-@ServiceProvider(service=StatisticsBuilder.class)
-public class ClusteringCoefficientBuilder implements StatisticsBuilder {
-
-    public String getName() {
-        return NbBundle.getMessage(ClusteringCoefficientBuilder.class, "ClusteringCoefficent.name");
-    }
-
-    public Statistics getStatistics() {
-        return new ClusteringCoefficient();
-    }
-
-    public Class<? extends Statistics> getStatisticsClass() {
-        return ClusteringCoefficient.class;
-    }
-}
+*/
+package org.gephi.statistics.plugin.builder;
+
+import org.gephi.statistics.plugin.ClusteringCoefficient;
+import org.gephi.statistics.spi.Statistics;
+import org.gephi.statistics.spi.StatisticsBuilder;
+import org.openide.util.NbBundle;
+import org.openide.util.lookup.ServiceProvider;
+
+/**
+ *
+ * @author pjmcswee
+ */
+@ServiceProvider(service=StatisticsBuilder.class)
+public class ClusteringCoefficientBuilder implements StatisticsBuilder {
+
+    @Override
+    public String getName() {
+        return NbBundle.getMessage(ClusteringCoefficientBuilder.class, "ClusteringCoefficent.name");
+    }
+
+    @Override
+    public Statistics getStatistics() {
+        return new ClusteringCoefficient();
+    }
+
+    @Override
+    public Class<? extends Statistics> getStatisticsClass() {
+        return ClusteringCoefficient.class;
+    }
+}

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/ConnectedComponentsBuilder.java

@@ -54,14 +54,17 @@ import org.openide.util.lookup.ServiceProvider;
 @ServiceProvider(service=StatisticsBuilder.class)
 public class ConnectedComponentsBuilder implements StatisticsBuilder {
 
+    @Override
     public String getName() {
         return NbBundle.getMessage(ConnectedComponentsBuilder.class, "ConnectedComponents.name");
     }
 
+    @Override
     public Statistics getStatistics() {
         return new ConnectedComponents();
     }
 
+    @Override
     public Class<? extends Statistics> getStatisticsClass() {
         return ConnectedComponents.class;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/DegreeBuilder.java

@@ -54,14 +54,17 @@ import org.openide.util.lookup.ServiceProvider;
 @ServiceProvider(service = StatisticsBuilder.class)
 public class DegreeBuilder implements StatisticsBuilder {
 
+    @Override
     public String getName() {
         return NbBundle.getMessage(DegreeBuilder.class, "InOutDegree.name");
     }
 
+    @Override
     public Statistics getStatistics() {
         return new Degree();
     }
 
+    @Override
     public Class<? extends Statistics> getStatisticsClass() {
         return Degree.class;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/DensityBuilder.java

@@ -38,31 +38,34 @@ made subject to such option by the copyright holder.
 Contributor(s):
 
 Portions Copyrighted 2011 Gephi Consortium.
-*/
-package org.gephi.statistics.plugin.builder;
-
-import org.gephi.statistics.plugin.GraphDensity;
-import org.gephi.statistics.spi.Statistics;
-import org.gephi.statistics.spi.StatisticsBuilder;
-import org.openide.util.NbBundle;
-import org.openide.util.lookup.ServiceProvider;
-
-/**
- * The statistics builder the graph denstiy statistics
- * @author pjmcswee
- */
-@ServiceProvider(service=StatisticsBuilder.class)
-public class DensityBuilder implements StatisticsBuilder {
-
-    public String getName() {
-        return NbBundle.getMessage(DensityBuilder.class, "GraphDensity.name");
-    }
-
-    public Statistics getStatistics() {
-        return new GraphDensity();
-    }
-
-    public Class<? extends Statistics> getStatisticsClass() {
-        return GraphDensity.class;
-    }
-}
+*/
+package org.gephi.statistics.plugin.builder;
+
+import org.gephi.statistics.plugin.GraphDensity;
+import org.gephi.statistics.spi.Statistics;
+import org.gephi.statistics.spi.StatisticsBuilder;
+import org.openide.util.NbBundle;
+import org.openide.util.lookup.ServiceProvider;
+
+/**
+ * The statistics builder the graph denstiy statistics
+ * @author pjmcswee
+ */
+@ServiceProvider(service=StatisticsBuilder.class)
+public class DensityBuilder implements StatisticsBuilder {
+
+    @Override
+    public String getName() {
+        return NbBundle.getMessage(DensityBuilder.class, "GraphDensity.name");
+    }
+
+    @Override
+    public Statistics getStatistics() {
+        return new GraphDensity();
+    }
+
+    @Override
+    public Class<? extends Statistics> getStatisticsClass() {
+        return GraphDensity.class;
+    }
+}

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/EigenvectorCentralityBuilder.java

@@ -38,32 +38,34 @@ made subject to such option by the copyright holder.
 Contributor(s):
 
 Portions Copyrighted 2011 Gephi Consortium.
-*/
-package org.gephi.statistics.plugin.builder;
-
-import org.gephi.statistics.plugin.EigenvectorCentrality;
-import org.gephi.statistics.plugin.Hits;
-import org.gephi.statistics.spi.Statistics;
-import org.gephi.statistics.spi.StatisticsBuilder;
-import org.openide.util.NbBundle;
-import org.openide.util.lookup.ServiceProvider;
-
-/**
- *
- * @author pjmcswee
- */
-@ServiceProvider(service = StatisticsBuilder.class)
-public class EigenvectorCentralityBuilder implements StatisticsBuilder {
-
-    public String getName() {
-        return NbBundle.getMessage(HitsBuilder.class, "EigenvectorCentrality.name");
-    }
-
-    public Statistics getStatistics() {
-        return new EigenvectorCentrality();
-    }
-
-    public Class<? extends Statistics> getStatisticsClass() {
-        return EigenvectorCentrality.class;
-    }
-}
+*/
+package org.gephi.statistics.plugin.builder;
+
+import org.gephi.statistics.plugin.EigenvectorCentrality;
+import org.gephi.statistics.spi.Statistics;
+import org.gephi.statistics.spi.StatisticsBuilder;
+import org.openide.util.NbBundle;
+import org.openide.util.lookup.ServiceProvider;
+
+/**
+ *
+ * @author pjmcswee
+ */
+@ServiceProvider(service = StatisticsBuilder.class)
+public class EigenvectorCentralityBuilder implements StatisticsBuilder {
+
+    @Override
+    public String getName() {
+        return NbBundle.getMessage(HitsBuilder.class, "EigenvectorCentrality.name");
+    }
+
+    @Override
+    public Statistics getStatistics() {
+        return new EigenvectorCentrality();
+    }
+
+    @Override
+    public Class<? extends Statistics> getStatisticsClass() {
+        return EigenvectorCentrality.class;
+    }
+}

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/GraphDistanceBuilder.java

@@ -38,31 +38,34 @@ made subject to such option by the copyright holder.
 Contributor(s):
 
 Portions Copyrighted 2011 Gephi Consortium.
-*/
-package org.gephi.statistics.plugin.builder;
-
-import org.gephi.statistics.plugin.GraphDistance;
-import org.gephi.statistics.spi.Statistics;
-import org.gephi.statistics.spi.StatisticsBuilder;
-import org.openide.util.NbBundle;
-import org.openide.util.lookup.ServiceProvider;
-
-/**
- *
- * @author pjmcswee
- */
-@ServiceProvider(service=StatisticsBuilder.class)
-public class GraphDistanceBuilder implements StatisticsBuilder {
-
-    public String getName() {
-        return NbBundle.getMessage(GraphDistanceBuilder.class, "GraphDistance.name");
-    }
-
-    public Statistics getStatistics() {
-        return new GraphDistance();
-    }
-
-    public Class<? extends Statistics> getStatisticsClass() {
-        return GraphDistance.class;
-    }
-}
+*/
+package org.gephi.statistics.plugin.builder;
+
+import org.gephi.statistics.plugin.GraphDistance;
+import org.gephi.statistics.spi.Statistics;
+import org.gephi.statistics.spi.StatisticsBuilder;
+import org.openide.util.NbBundle;
+import org.openide.util.lookup.ServiceProvider;
+
+/**
+ *
+ * @author pjmcswee
+ */
+@ServiceProvider(service=StatisticsBuilder.class)
+public class GraphDistanceBuilder implements StatisticsBuilder {
+
+    @Override
+    public String getName() {
+        return NbBundle.getMessage(GraphDistanceBuilder.class, "GraphDistance.name");
+    }
+
+    @Override
+    public Statistics getStatistics() {
+        return new GraphDistance();
+    }
+
+    @Override
+    public Class<? extends Statistics> getStatisticsClass() {
+        return GraphDistance.class;
+    }
+}

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/HitsBuilder.java

@@ -38,31 +38,34 @@ made subject to such option by the copyright holder.
 Contributor(s):
 
 Portions Copyrighted 2011 Gephi Consortium.
-*/
-package org.gephi.statistics.plugin.builder;
-
-import org.gephi.statistics.plugin.Hits;
-import org.gephi.statistics.spi.Statistics;
-import org.gephi.statistics.spi.StatisticsBuilder;
-import org.openide.util.NbBundle;
-import org.openide.util.lookup.ServiceProvider;
-
-/**
- *
- * @author pjmcswee
- */
-@ServiceProvider(service = StatisticsBuilder.class)
-public class HitsBuilder implements StatisticsBuilder {
-
-    public String getName() {
-        return NbBundle.getMessage(HitsBuilder.class, "Hits.name");
-    }
-
-    public Statistics getStatistics() {
-        return new Hits();
-    }
-
-    public Class<? extends Statistics> getStatisticsClass() {
-        return Hits.class;
-    }
-}
+*/
+package org.gephi.statistics.plugin.builder;
+
+import org.gephi.statistics.plugin.Hits;
+import org.gephi.statistics.spi.Statistics;
+import org.gephi.statistics.spi.StatisticsBuilder;
+import org.openide.util.NbBundle;
+import org.openide.util.lookup.ServiceProvider;
+
+/**
+ *
+ * @author pjmcswee
+ */
+@ServiceProvider(service = StatisticsBuilder.class)
+public class HitsBuilder implements StatisticsBuilder {
+
+    @Override
+    public String getName() {
+        return NbBundle.getMessage(HitsBuilder.class, "Hits.name");
+    }
+
+    @Override
+    public Statistics getStatistics() {
+        return new Hits();
+    }
+
+    @Override
+    public Class<? extends Statistics> getStatisticsClass() {
+        return Hits.class;
+    }
+}

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/ModularityBuilder.java

@@ -38,31 +38,34 @@ made subject to such option by the copyright holder.
 Contributor(s):
 
 Portions Copyrighted 2011 Gephi Consortium.
-*/
-package org.gephi.statistics.plugin.builder;
-
-import org.gephi.statistics.plugin.Modularity;
-import org.gephi.statistics.spi.Statistics;
-import org.gephi.statistics.spi.StatisticsBuilder;
-import org.openide.util.NbBundle;
-import org.openide.util.lookup.ServiceProvider;
-
-/**
- *
- * @author pjmcswee
- */
-@ServiceProvider(service = StatisticsBuilder.class)
-public class ModularityBuilder implements StatisticsBuilder {
-
-    public String getName() {
-        return NbBundle.getMessage(ModularityBuilder.class, "Modularity.name");
-    }
-
-    public Statistics getStatistics() {
-        return new Modularity();
-    }
-
-    public Class<? extends Statistics> getStatisticsClass() {
-        return Modularity.class;
-    }
-}
+*/
+package org.gephi.statistics.plugin.builder;
+
+import org.gephi.statistics.plugin.Modularity;
+import org.gephi.statistics.spi.Statistics;
+import org.gephi.statistics.spi.StatisticsBuilder;
+import org.openide.util.NbBundle;
+import org.openide.util.lookup.ServiceProvider;
+
+/**
+ *
+ * @author pjmcswee
+ */
+@ServiceProvider(service = StatisticsBuilder.class)
+public class ModularityBuilder implements StatisticsBuilder {
+
+    @Override
+    public String getName() {
+        return NbBundle.getMessage(ModularityBuilder.class, "Modularity.name");
+    }
+
+    @Override
+    public Statistics getStatistics() {
+        return new Modularity();
+    }
+
+    @Override
+    public Class<? extends Statistics> getStatisticsClass() {
+        return Modularity.class;
+    }
+}

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/PageRankBuilder.java

@@ -38,31 +38,34 @@ made subject to such option by the copyright holder.
 Contributor(s):
 
 Portions Copyrighted 2011 Gephi Consortium.
-*/
-package org.gephi.statistics.plugin.builder;
-
-import org.gephi.statistics.plugin.PageRank;
-import org.gephi.statistics.spi.Statistics;
-import org.gephi.statistics.spi.StatisticsBuilder;
-import org.openide.util.NbBundle;
-import org.openide.util.lookup.ServiceProvider;
-
-/**
- *
- * @author pjmcswee
- */
-@ServiceProvider(service = StatisticsBuilder.class)
-public class PageRankBuilder implements StatisticsBuilder {
-
-    public String getName() {
-        return NbBundle.getMessage(PageRankBuilder.class, "PageRank.name");
-    }
-
-    public Statistics getStatistics() {
-        return new PageRank();
-    }
-
-    public Class<? extends Statistics> getStatisticsClass() {
-        return PageRank.class;
-    }
-}
+*/
+package org.gephi.statistics.plugin.builder;
+
+import org.gephi.statistics.plugin.PageRank;
+import org.gephi.statistics.spi.Statistics;
+import org.gephi.statistics.spi.StatisticsBuilder;
+import org.openide.util.NbBundle;
+import org.openide.util.lookup.ServiceProvider;
+
+/**
+ *
+ * @author pjmcswee
+ */
+@ServiceProvider(service = StatisticsBuilder.class)
+public class PageRankBuilder implements StatisticsBuilder {
+
+    @Override
+    public String getName() {
+        return NbBundle.getMessage(PageRankBuilder.class, "PageRank.name");
+    }
+
+    @Override
+    public Statistics getStatistics() {
+        return new PageRank();
+    }
+
+    @Override
+    public Class<? extends Statistics> getStatisticsClass() {
+        return PageRank.class;
+    }
+}

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/builder/WeightedDegreeBuilder.java

@@ -54,14 +54,17 @@ import org.openide.util.lookup.ServiceProvider;
 @ServiceProvider(service = StatisticsBuilder.class)
 public class WeightedDegreeBuilder implements StatisticsBuilder {
 
+    @Override
     public String getName() {
         return NbBundle.getMessage(WeightedDegreeBuilder.class, "WeightedDegree.name");
     }
 
+    @Override
     public Statistics getStatistics() {
         return new WeightedDegree();
     }
 
+    @Override
     public Class<? extends Statistics> getStatisticsClass() {
         return WeightedDegree.class;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/dynamic/DynamicClusteringCoefficient.java

@@ -45,19 +45,15 @@ import java.text.DecimalFormat;
 import java.text.NumberFormat;
 import java.util.HashMap;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeType;
-import org.gephi.data.attributes.type.DynamicDouble;
-import org.gephi.data.attributes.type.Interval;
-import org.gephi.dynamic.api.DynamicController;
-import org.gephi.dynamic.api.DynamicModel;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
+import org.gephi.attribute.time.Interval;
+import org.gephi.attribute.time.TimestampDoubleSet;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphController;
 import org.gephi.graph.api.GraphModel;
 import org.gephi.graph.api.GraphView;
-import org.gephi.graph.api.HierarchicalGraph;
 import org.gephi.graph.api.Node;
 import org.gephi.statistics.plugin.ChartUtils;
 import org.gephi.statistics.plugin.ClusteringCoefficient;
@@ -90,48 +86,38 @@ public class DynamicClusteringCoefficient implements DynamicStatistics, LongTask
     private boolean cancel = false;
     private ClusteringCoefficient clusteringCoefficientStat;
     //Cols
-    private AttributeColumn dynamicCoefficientColumn;
+    private Column dynamicCoefficientColumn;
     //Average
-    private AttributeColumn dynamicAverageCoefficientColumn;
-    private DynamicDouble averages;
+    private Column dynamicAverageCoefficientColumn;
+    private Map<Double, Double> averages;
 
     public DynamicClusteringCoefficient() {
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            isDirected = graphController.getModel().isDirected();
+        if (graphController != null && graphController.getGraphModel()!= null) {
+            isDirected = graphController.getGraphModel().isDirected();
         }
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
         this.graphModel = graphModel;
         this.isDirected = graphModel.isDirected();
+        this.averages = new HashMap<Double, Double>();
 
         //Attributes cols
         if (!averageOnly) {
-            AttributeTable nodeTable = attributeModel.getNodeTable();
+            Table nodeTable = attributeModel.getNodeTable();
             dynamicCoefficientColumn = nodeTable.getColumn(DYNAMIC_CLUSTERING_COEFFICIENT);
             if (dynamicCoefficientColumn == null) {
-                dynamicCoefficientColumn = nodeTable.addColumn(DYNAMIC_CLUSTERING_COEFFICIENT, NbBundle.getMessage(DynamicClusteringCoefficient.class, "DynamicClusteringCoefficient.nodecolumn.ClusteringCoefficient"), AttributeType.DYNAMIC_DOUBLE, AttributeOrigin.COMPUTED, new DynamicDouble());
+                dynamicCoefficientColumn = nodeTable.addColumn(DYNAMIC_CLUSTERING_COEFFICIENT, NbBundle.getMessage(DynamicClusteringCoefficient.class, "DynamicClusteringCoefficient.nodecolumn.ClusteringCoefficient"), TimestampDoubleSet.class, null);
             }
         }
-
-        //Column
-        AttributeTable graphTable = attributeModel.getGraphTable();
-        dynamicAverageCoefficientColumn = graphTable.getColumn(DYNAMIC_AVG_CLUSTERING_COEFFICIENT);
-        if (dynamicAverageCoefficientColumn == null) {
-            dynamicAverageCoefficientColumn = graphTable.addColumn(DYNAMIC_AVG_CLUSTERING_COEFFICIENT, NbBundle.getMessage(DynamicClusteringCoefficient.class, "DynamicClusteringCoefficient.graphcolumn.AvgClusteringCoefficient"), AttributeType.DYNAMIC_DOUBLE, AttributeOrigin.COMPUTED, new DynamicDouble());
-        }
     }
 
+    @Override
     public String getReport() {
-        //Transform to Map
-        Map<Double, Double> map = new HashMap<Double, Double>();
-        for (Interval<Double> interval : averages.getIntervals()) {
-            map.put(interval.getLow(), interval.getValue());
-        }
-
         //Time series
-        XYSeries dSeries = ChartUtils.createXYSeries(map, "Clustering Coefficient Time Series");
+        XYSeries dSeries = ChartUtils.createXYSeries(averages, "Clustering Coefficient Time Series");
 
         XYSeriesCollection dataset = new XYSeriesCollection();
         dataset.addSeries(dSeries);
@@ -168,12 +154,13 @@ public class DynamicClusteringCoefficient implements DynamicStatistics, LongTask
         return report;
     }
 
+    @Override
     public void loop(GraphView window, Interval interval) {
-        HierarchicalGraph graph = null;
+        Graph graph = null;
         if (isDirected) {
-            graph = graphModel.getHierarchicalDirectedGraph(window);
+            graph = graphModel.getDirectedGraph(window);
         } else {
-            graph = graphModel.getHierarchicalUndirectedGraph(window);
+            graph = graphModel.getUndirectedGraph(window);
         }
 
         graph.readLock();
@@ -188,14 +175,10 @@ public class DynamicClusteringCoefficient implements DynamicStatistics, LongTask
             int i = 0;
             for (Node n : graph.getNodes()) {
                 double coef = coefficients[i++];
-                Interval<Double> valInterval = new Interval<Double>(interval, coef);
-                DynamicDouble val = (DynamicDouble) n.getAttributes().getValue(dynamicCoefficientColumn.getIndex());
-                if (val == null) {
-                    val = new DynamicDouble(valInterval);
-                } else {
-                    val = new DynamicDouble(val, valInterval);
-                }
-                n.getAttributes().setValue(dynamicCoefficientColumn.getIndex(), val);
+                
+                n.setAttribute(dynamicCoefficientColumn, coef, interval.getLow());
+                n.setAttribute(dynamicCoefficientColumn, coef, interval.getHigh());
+                
                 if (cancel) {
                     break;
                 }
@@ -206,36 +189,44 @@ public class DynamicClusteringCoefficient implements DynamicStatistics, LongTask
 
         //Average
         double avg = clusteringCoefficientStat.getAverageClusteringCoefficient();
+        graph.setAttribute(DYNAMIC_AVG_CLUSTERING_COEFFICIENT, avg, interval.getLow());
+        graph.setAttribute(DYNAMIC_AVG_CLUSTERING_COEFFICIENT, avg, interval.getHigh());
 
-        averages = new DynamicDouble(averages, new Interval<Double>(interval.getLow(), interval.getHigh(), false, true, avg));
+        averages.put(interval.getLow(), avg);
+        averages.put(interval.getHigh(), avg);
     }
 
+    @Override
     public void end() {
         clusteringCoefficientStat = null;
-
-        graphModel.getGraphVisible().getAttributes().setValue(dynamicAverageCoefficientColumn.getIndex(), averages);
     }
 
+    @Override
     public void setBounds(Interval bounds) {
         this.bounds = bounds;
     }
 
+    @Override
     public void setWindow(double window) {
         this.window = window;
     }
 
+    @Override
     public void setTick(double tick) {
         this.tick = tick;
     }
 
+    @Override
     public double getWindow() {
         return window;
     }
 
+    @Override
     public double getTick() {
         return tick;
     }
 
+    @Override
     public Interval getBounds() {
         return bounds;
     }
@@ -256,11 +247,13 @@ public class DynamicClusteringCoefficient implements DynamicStatistics, LongTask
         return averageOnly;
     }
 
+    @Override
     public boolean cancel() {
         cancel = true;
         return true;
     }
 
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
     }
 }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/dynamic/DynamicDegree.java

@@ -1,43 +1,43 @@
 /*
-Copyright 2008-2010 Gephi
-Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2010 Gephi
+ Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s):
+ Contributor(s):
 
-Portions Copyrighted 2011 Gephi Consortium.
+ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics.plugin.dynamic;
 
@@ -45,19 +45,17 @@ import java.text.DecimalFormat;
 import java.text.NumberFormat;
 import java.util.HashMap;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeType;
-import org.gephi.data.attributes.type.DynamicDouble;
-import org.gephi.data.attributes.type.DynamicInteger;
-import org.gephi.data.attributes.type.Interval;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
+import org.gephi.attribute.time.Interval;
+import org.gephi.attribute.time.TimestampDoubleSet;
+import org.gephi.attribute.time.TimestampIntegerSet;
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphController;
 import org.gephi.graph.api.GraphModel;
 import org.gephi.graph.api.GraphView;
-import org.gephi.graph.api.HierarchicalDirectedGraph;
-import org.gephi.graph.api.HierarchicalGraph;
 import org.gephi.graph.api.Node;
 import org.gephi.statistics.plugin.ChartUtils;
 import org.gephi.statistics.spi.DynamicStatistics;
@@ -90,60 +88,49 @@ public class DynamicDegree implements DynamicStatistics, LongTask {
     private boolean averageOnly;
     private boolean cancel = false;
     //Cols
-    private AttributeColumn dynamicInDegreeColumn;
-    private AttributeColumn dynamicOutDegreeColumn;
-    private AttributeColumn dynamicDegreeColumn;
+    private Column dynamicInDegreeColumn;
+    private Column dynamicOutDegreeColumn;
+    private Column dynamicDegreeColumn;
     //Average
-    private AttributeColumn dynamicAverageDegreeColumn;
-    private DynamicDouble averages;
+    private Map<Double, Double> averages;
 
     public DynamicDegree() {
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            isDirected = graphController.getModel().isDirected();
+        if (graphController != null && graphController.getGraphModel() != null) {
+            isDirected = graphController.getGraphModel().isDirected();
         }
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
         this.graphModel = graphModel;
         this.isDirected = graphModel.isDirected();
+        this.averages = new HashMap<Double, Double>();
 
         //Attributes cols
         if (!averageOnly) {
-            AttributeTable nodeTable = attributeModel.getNodeTable();
+            Table nodeTable = attributeModel.getNodeTable();
             dynamicInDegreeColumn = nodeTable.getColumn(DYNAMIC_INDEGREE);
             dynamicOutDegreeColumn = nodeTable.getColumn(DYNAMIC_OUTDEGREE);
             dynamicDegreeColumn = nodeTable.getColumn(DYNAMIC_DEGREE);
             if (isDirected) {
                 if (dynamicInDegreeColumn == null) {
-                    dynamicInDegreeColumn = nodeTable.addColumn(DYNAMIC_INDEGREE, NbBundle.getMessage(DynamicDegree.class, "DynamicDegree.nodecolumn.InDegree"), AttributeType.DYNAMIC_INT, AttributeOrigin.COMPUTED, new DynamicInteger());
+                    dynamicInDegreeColumn = nodeTable.addColumn(DYNAMIC_INDEGREE, NbBundle.getMessage(DynamicDegree.class, "DynamicDegree.nodecolumn.InDegree"), TimestampIntegerSet.class, null);
                 }
                 if (dynamicOutDegreeColumn == null) {
-                    dynamicOutDegreeColumn = nodeTable.addColumn(DYNAMIC_OUTDEGREE, NbBundle.getMessage(DynamicDegree.class, "DynamicDegree.nodecolumn.OutDegree"), AttributeType.DYNAMIC_INT, AttributeOrigin.COMPUTED, new DynamicInteger());
+                    dynamicOutDegreeColumn = nodeTable.addColumn(DYNAMIC_OUTDEGREE, NbBundle.getMessage(DynamicDegree.class, "DynamicDegree.nodecolumn.OutDegree"), TimestampIntegerSet.class, null);
                 }
             }
             if (dynamicDegreeColumn == null) {
-                dynamicDegreeColumn = nodeTable.addColumn(DYNAMIC_DEGREE, NbBundle.getMessage(DynamicDegree.class, "DynamicDegree.nodecolumn.Degree"), AttributeType.DYNAMIC_INT, AttributeOrigin.COMPUTED, new DynamicInteger());
+                dynamicDegreeColumn = nodeTable.addColumn(DYNAMIC_DEGREE, NbBundle.getMessage(DynamicDegree.class, "DynamicDegree.nodecolumn.Degree"), TimestampIntegerSet.class, null);
             }
         }
-
-        //Avg Column
-        AttributeTable graphTable = attributeModel.getGraphTable();
-        dynamicAverageDegreeColumn = graphTable.getColumn(DYNAMIC_AVGDEGREE);
-        if (dynamicAverageDegreeColumn == null) {
-            dynamicAverageDegreeColumn = graphTable.addColumn(DYNAMIC_AVGDEGREE, NbBundle.getMessage(DynamicDegree.class, "DynamicDegree.graphcolumn.AvgDegree"), AttributeType.DYNAMIC_DOUBLE, AttributeOrigin.COMPUTED, new DynamicDouble());
-        }
     }
 
+    @Override
     public String getReport() {
-        //Transform to Map
-        Map<Double, Double> map = new HashMap<Double, Double>();
-        for (Interval<Double> interval : averages.getIntervals()) {
-            map.put(interval.getLow(), interval.getValue());
-        }
-
         //Time series
-        XYSeries dSeries = ChartUtils.createXYSeries(map, "Degree Time Series");
+        XYSeries dSeries = ChartUtils.createXYSeries(averages, "Degree Time Series");
 
         XYSeriesCollection dataset = new XYSeriesCollection();
         dataset.addSeries(dSeries);
@@ -174,53 +161,33 @@ public class DynamicDegree implements DynamicStatistics, LongTask {
                 + "<br /><br />" + degreeImageFile;
 
         /*for (Interval<Double> averages : averages) {
-        report += averages.toString(dynamicModel.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) + "<br />";
-        }*/
+         report += averages.toString(dynamicModel.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) + "<br />";
+         }*/
         report += "<br /><br /></BODY></HTML>";
         return report;
     }
 
+    @Override
     public void loop(GraphView window, Interval interval) {
-        HierarchicalGraph graph = graphModel.getHierarchicalGraph(window);
-        HierarchicalDirectedGraph directedGraph = null;
+        Graph graph = graphModel.getGraph(window);
+        DirectedGraph directedGraph = null;
         if (isDirected) {
-            directedGraph = graphModel.getHierarchicalDirectedGraph(window);
+            directedGraph = graphModel.getDirectedGraph(window);
         }
 
         long sum = 0;
         for (Node n : graph.getNodes().toArray()) {
-            int degree = graph.getTotalDegree(n);
+            int degree = graph.getDegree(n);
 
             if (!averageOnly) {
-                Interval<Integer> degreeInInterval = new Interval<Integer>(interval, degree);
-                DynamicInteger val = (DynamicInteger) n.getAttributes().getValue(dynamicDegreeColumn.getIndex());
-                if (val == null) {
-                    val = new DynamicInteger(degreeInInterval);
-                } else {
-                    val = new DynamicInteger(val, degreeInInterval);
-                }
-                n.getAttributes().setValue(dynamicDegreeColumn.getIndex(), val);
+                n.setAttribute(dynamicDegreeColumn, degree, interval.getLow());
 
                 if (isDirected) {
-                    int indegree = directedGraph.getTotalInDegree(n);
-                    Interval<Integer> inDegreeInInterval = new Interval<Integer>(interval, indegree);
-                    DynamicInteger inVal = (DynamicInteger) n.getAttributes().getValue(dynamicInDegreeColumn.getIndex());
-                    if (inVal == null) {
-                        inVal = new DynamicInteger(inDegreeInInterval);
-                    } else {
-                        inVal = new DynamicInteger(inVal, inDegreeInInterval);
-                    }
-                    n.getAttributes().setValue(dynamicInDegreeColumn.getIndex(), inVal);
+                    int indegree = directedGraph.getInDegree(n);
+                    n.setAttribute(dynamicInDegreeColumn, indegree, interval.getLow());
 
-                    int outdegree = directedGraph.getTotalOutDegree(n);
-                    Interval<Integer> outDegreeInInterval = new Interval<Integer>(interval, outdegree);
-                    DynamicInteger outVal = (DynamicInteger) n.getAttributes().getValue(dynamicOutDegreeColumn.getIndex());
-                    if (outVal == null) {
-                        outVal = new DynamicInteger(outDegreeInInterval);
-                    } else {
-                        outVal = new DynamicInteger(outVal, outDegreeInInterval);
-                    }
-                    n.getAttributes().setValue(dynamicOutDegreeColumn.getIndex(), outVal);
+                    int outdegree = directedGraph.getOutDegree(n);
+                    n.setAttribute(dynamicOutDegreeColumn, outdegree, interval.getLow());
                 }
             }
             sum += degree;
@@ -230,34 +197,43 @@ public class DynamicDegree implements DynamicStatistics, LongTask {
         }
 
         double avg = sum / (double) graph.getNodeCount();
-
-        averages = new DynamicDouble(averages, new Interval<Double>(interval.getLow(), interval.getHigh(), false, true, avg));
+        averages.put(interval.getLow(), avg);
+        averages.put(interval.getHigh(), avg);
+        
+        graph.setAttribute(DYNAMIC_AVGDEGREE, avg, interval.getLow());
+        graph.setAttribute(DYNAMIC_AVGDEGREE, avg, interval.getHigh());
     }
 
+    @Override
     public void end() {
-        graphModel.getGraphVisible().getAttributes().setValue(dynamicAverageDegreeColumn.getIndex(), averages);
     }
 
+    @Override
     public void setBounds(Interval bounds) {
         this.bounds = bounds;
     }
 
+    @Override
     public void setWindow(double window) {
         this.window = window;
     }
 
+    @Override
     public void setTick(double tick) {
         this.tick = tick;
     }
 
+    @Override
     public double getWindow() {
         return window;
     }
 
+    @Override
     public double getTick() {
         return tick;
     }
 
+    @Override
     public Interval getBounds() {
         return bounds;
     }
@@ -278,11 +254,13 @@ public class DynamicDegree implements DynamicStatistics, LongTask {
         return averageOnly;
     }
 
+    @Override
     public boolean cancel() {
         cancel = true;
         return true;
     }
 
+    @Override
     public void setProgressTicket(ProgressTicket progressTicket) {
     }
 }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/dynamic/DynamicNbEdges.java

@@ -45,16 +45,11 @@ import java.text.DecimalFormat;
 import java.text.NumberFormat;
 import java.util.HashMap;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeType;
-import org.gephi.data.attributes.type.DynamicInteger;
-import org.gephi.data.attributes.type.Interval;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.time.Interval;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphModel;
 import org.gephi.graph.api.GraphView;
-import org.gephi.graph.api.HierarchicalGraph;
 import org.gephi.statistics.plugin.ChartUtils;
 import org.gephi.statistics.spi.DynamicStatistics;
 import org.jfree.chart.ChartFactory;
@@ -62,7 +57,6 @@ import org.jfree.chart.JFreeChart;
 import org.jfree.chart.plot.PlotOrientation;
 import org.jfree.data.xy.XYSeries;
 import org.jfree.data.xy.XYSeriesCollection;
-import org.openide.util.NbBundle;
 
 /**
  *
@@ -77,29 +71,18 @@ public class DynamicNbEdges implements DynamicStatistics {
     private double tick;
     private Interval bounds;
     //Average
-    private AttributeColumn nbEdgesCol;
-    private DynamicInteger counts;
+    private Map<Double, Integer> counts;
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
         this.graphModel = graphModel;
-
-        //Column
-        AttributeTable graphTable = attributeModel.getGraphTable();
-        nbEdgesCol = graphTable.getColumn(NB_EDGES);
-        if (nbEdgesCol == null) {
-            nbEdgesCol = graphTable.addColumn(NB_EDGES, NbBundle.getMessage(DynamicNbEdges.class, "DynamicNbNodes.graphcolumn.NbEdges"), AttributeType.DYNAMIC_INT, AttributeOrigin.COMPUTED, new DynamicInteger());
-        }
+        this.counts = new HashMap<Double, Integer>();
     }
 
+    @Override
     public String getReport() {
-        //Transform to Map
-        Map<Double, Integer> map = new HashMap<Double, Integer>();
-        for(Interval<Integer> interval : counts.getIntervals()) {
-            map.put(interval.getLow(), interval.getValue());
-        }
-        
         //Time series
-        XYSeries dSeries = ChartUtils.createXYSeries(map, "Nb Edges Time Series");
+        XYSeries dSeries = ChartUtils.createXYSeries(counts, "Nb Edges Time Series");
 
         XYSeriesCollection dataset = new XYSeriesCollection();
         dataset.addSeries(dSeries);
@@ -136,38 +119,48 @@ public class DynamicNbEdges implements DynamicStatistics {
         return report;
     }
 
+    @Override
     public void loop(GraphView window, Interval interval) {
-        HierarchicalGraph graph = graphModel.getHierarchicalGraph(window);
+        Graph graph = graphModel.getGraph(window);
 
         int count = graph.getEdgeCount();
+        
+        graph.setAttribute(NB_EDGES, count, interval.getLow());
+        graph.setAttribute(NB_EDGES, count, interval.getHigh());
 
-        counts = new DynamicInteger(counts, new Interval<Integer>(interval.getLow(), interval.getHigh(), false, true, count));
+        counts.put(interval.getLow(), count);
+        counts.put(interval.getHigh(), count);
     }
 
+    @Override
     public void end() {
-        graphModel.getGraphVisible().getAttributes().setValue(nbEdgesCol.getIndex(), counts);
     }
 
     public void setBounds(Interval bounds) {
         this.bounds = bounds;
     }
 
+    @Override
     public void setWindow(double window) {
         this.window = window;
     }
 
+    @Override
     public void setTick(double tick) {
         this.tick = tick;
     }
 
+    @Override
     public double getWindow() {
         return window;
     }
 
+    @Override
     public double getTick() {
         return tick;
     }
 
+    @Override
     public Interval getBounds() {
         return bounds;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/dynamic/DynamicNbNodes.java

@@ -1,43 +1,43 @@
 /*
-Copyright 2008-2011 Gephi
-Authors : Sébastien Heymann <sebastien.heymann@gephi.org>
-Website : http://www.gephi.org
+ Copyright 2008-2011 Gephi
+ Authors : Sébastien Heymann <sebastien.heymann@gephi.org>
+ Website : http://www.gephi.org
 
-This file is part of Gephi.
+ This file is part of Gephi.
 
-DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
 
-Copyright 2011 Gephi Consortium. All rights reserved.
+ Copyright 2011 Gephi Consortium. All rights reserved.
 
-The contents of this file are subject to the terms of either the GNU
-General Public License Version 3 only ("GPL") or the Common
-Development and Distribution License("CDDL") (collectively, the
-"License"). You may not use this file except in compliance with the
-License. You can obtain a copy of the License at
-http://gephi.org/about/legal/license-notice/
-or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
-specific language governing permissions and limitations under the
-License.  When distributing the software, include this License Header
-Notice in each file and include the License files at
-/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
-License Header, with the fields enclosed by brackets [] replaced by
-your own identifying information:
-"Portions Copyrighted [year] [name of copyright owner]"
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
 
-If you wish your version of this file to be governed by only the CDDL
-or only the GPL Version 3, indicate your decision by adding
-"[Contributor] elects to include this software in this distribution
-under the [CDDL or GPL Version 3] license." If you do not indicate a
-single choice of license, a recipient has the option to distribute
-your version of this file under either the CDDL, the GPL Version 3 or
-to extend the choice of license to its licensees as provided above.
-However, if you add GPL Version 3 code and therefore, elected the GPL
-Version 3 license, then the option applies only if the new code is
-made subject to such option by the copyright holder.
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
 
-Contributor(s):
+ Contributor(s):
 
-Portions Copyrighted 2011 Gephi Consortium.
+ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.statistics.plugin.dynamic;
 
@@ -45,16 +45,11 @@ import java.text.DecimalFormat;
 import java.text.NumberFormat;
 import java.util.HashMap;
 import java.util.Map;
-import org.gephi.data.attributes.api.AttributeColumn;
-import org.gephi.data.attributes.api.AttributeModel;
-import org.gephi.data.attributes.api.AttributeOrigin;
-import org.gephi.data.attributes.api.AttributeTable;
-import org.gephi.data.attributes.api.AttributeType;
-import org.gephi.data.attributes.type.DynamicInteger;
-import org.gephi.data.attributes.type.Interval;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.time.Interval;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphModel;
 import org.gephi.graph.api.GraphView;
-import org.gephi.graph.api.HierarchicalGraph;
 import org.gephi.statistics.plugin.ChartUtils;
 import org.gephi.statistics.spi.DynamicStatistics;
 import org.jfree.chart.ChartFactory;
@@ -62,7 +57,6 @@ import org.jfree.chart.JFreeChart;
 import org.jfree.chart.plot.PlotOrientation;
 import org.jfree.data.xy.XYSeries;
 import org.jfree.data.xy.XYSeriesCollection;
-import org.openide.util.NbBundle;
 
 /**
  *
@@ -77,31 +71,18 @@ public class DynamicNbNodes implements DynamicStatistics {
     private double tick;
     private Interval bounds;
     //Average
-    private AttributeColumn nbNodesCol;
-    private DynamicInteger counts;
+    private Map<Double, Integer> counts;
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
         this.graphModel = graphModel;
-
-        //Column
-        AttributeTable graphTable = attributeModel.getGraphTable();
-        nbNodesCol = graphTable.getColumn(NB_NODES);
-        if (nbNodesCol == null) {
-            nbNodesCol = graphTable.addColumn(NB_NODES, NbBundle.getMessage(DynamicNbNodes.class, "DynamicNbNodes.graphcolumn.NbNodes"), AttributeType.DYNAMIC_INT, AttributeOrigin.COMPUTED, new DynamicInteger());
-        }
-        counts = new DynamicInteger();
-        graphModel.getGraphVisible().getAttributes().setValue(nbNodesCol.getIndex(), counts);
+        this.counts = new HashMap<Double, Integer>();
     }
 
+    @Override
     public String getReport() {
-        //Transform to Map
-        Map<Double, Integer> map = new HashMap<Double, Integer>();
-        for (Interval<Integer> interval : counts.getIntervals()) {
-            map.put(interval.getLow(), interval.getValue());
-        }
-
         //Time series
-        XYSeries dSeries = ChartUtils.createXYSeries(map, "Nb Nodes Time Series");
+        XYSeries dSeries = ChartUtils.createXYSeries(counts, "Nb Nodes Time Series");
 
         XYSeriesCollection dataset = new XYSeriesCollection();
         dataset.addSeries(dSeries);
@@ -132,44 +113,55 @@ public class DynamicNbNodes implements DynamicStatistics {
                 + "<br /><br />" + imageFile;
 
         /*for (Interval<Integer> count : counts) {
-        report += count.toString(dynamicModel.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) + "<br />";
-        }*/
+         report += count.toString(dynamicModel.getTimeFormat().equals(DynamicModel.TimeFormat.DOUBLE)) + "<br />";
+         }*/
         report += "<br /><br /></BODY></HTML>";
         return report;
     }
 
+    @Override
     public void loop(GraphView window, Interval interval) {
-        HierarchicalGraph graph = graphModel.getHierarchicalGraph(window);
+        Graph graph = graphModel.getGraph(window);
 
         int count = graph.getNodeCount();
 
-        counts = new DynamicInteger(counts, new Interval<Integer>(interval.getLow(), interval.getHigh(), false, true, count));
+        graph.setAttribute(NB_NODES, count, interval.getLow());
+        graph.setAttribute(NB_NODES, count, interval.getHigh());
+
+        counts.put(interval.getLow(), count);
+        counts.put(interval.getHigh(), count);
     }
 
+    @Override
     public void end() {
-        graphModel.getGraphVisible().getAttributes().setValue(nbNodesCol.getIndex(), counts);
     }
 
+    @Override
     public void setBounds(Interval bounds) {
         this.bounds = bounds;
     }
 
+    @Override
     public void setWindow(double window) {
         this.window = window;
     }
 
+    @Override
     public void setTick(double tick) {
         this.tick = tick;
     }
 
+    @Override
     public double getWindow() {
         return window;
     }
 
+    @Override
     public double getTick() {
         return tick;
     }
 
+    @Override
     public Interval getBounds() {
         return bounds;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/dynamic/builder/DynamicClusteringCoefficientBuilder.java

@@ -54,14 +54,17 @@ import org.openide.util.lookup.ServiceProvider;
 @ServiceProvider(service = StatisticsBuilder.class)
 public class DynamicClusteringCoefficientBuilder implements StatisticsBuilder {
 
+    @Override
     public String getName() {
         return NbBundle.getMessage(DynamicClusteringCoefficientBuilder.class, "DynamicClusteringCoefficient.name");
     }
 
+    @Override
     public Statistics getStatistics() {
         return new DynamicClusteringCoefficient();
     }
 
+    @Override
     public Class<? extends Statistics> getStatisticsClass() {
         return DynamicClusteringCoefficient.class;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/dynamic/builder/DynamicDegreeBuilder.java

@@ -54,14 +54,17 @@ import org.openide.util.lookup.ServiceProvider;
 @ServiceProvider(service = StatisticsBuilder.class)
 public class DynamicDegreeBuilder implements StatisticsBuilder {
 
+    @Override
     public String getName() {
         return NbBundle.getMessage(DynamicDegreeBuilder.class, "DynamicDegree.name");
     }
 
+    @Override
     public Statistics getStatistics() {
         return new DynamicDegree();
     }
 
+    @Override
     public Class<? extends Statistics> getStatisticsClass() {
         return DynamicDegree.class;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/dynamic/builder/DynamicNbEdgesBuilder.java

@@ -54,14 +54,17 @@ import org.openide.util.lookup.ServiceProvider;
 @ServiceProvider(service = StatisticsBuilder.class)
 public class DynamicNbEdgesBuilder implements StatisticsBuilder {
 
+    @Override
     public String getName() {
         return NbBundle.getMessage(DynamicNbNodesBuilder.class, "DynamicNbEdges.name");
     }
 
+    @Override
     public Statistics getStatistics() {
         return new DynamicNbEdges();
     }
 
+    @Override
     public Class<? extends Statistics> getStatisticsClass() {
         return DynamicNbEdges.class;
     }

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/dynamic/builder/DynamicNbNodesBuilder.java

@@ -54,14 +54,17 @@ import org.openide.util.lookup.ServiceProvider;
 @ServiceProvider(service = StatisticsBuilder.class)
 public class DynamicNbNodesBuilder implements StatisticsBuilder {
 
+    @Override
     public String getName() {
         return NbBundle.getMessage(DynamicNbNodesBuilder.class, "DynamicNbNodes.name");
     }
 
+    @Override
     public Statistics getStatistics() {
         return new DynamicNbNodes();
     }
 
+    @Override
     public Class<? extends Statistics> getStatisticsClass() {
         return DynamicNbNodes.class;
     }

modules/StatisticsPlugin/src/main/resources/org/gephi/statistics/plugin/Bundle.properties

@@ -7,4 +7,8 @@ OpenIDE-Module-Short-Description=Standard statistics and metrics algorithms
 Degree.nodecolumn.InDegree = In-Degree
 Degree.nodecolumn.OutDegree = Out-Degree
 Degree.nodecolumn.Degree = Degree
-Degree.graphcolumn.AverageDegree = Average Degree
+Degree.graphcolumn.AverageDegree = Average Degree
+
+WeightedDegree.nodecolumn.InDegree = Weighted In-Degree
+WeightedDegree.nodecolumn.OutDegree = Weighted Out-Degree
+WeightedDegree.nodecolumn.Degree = Weighted Degree

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/ClusteringCoefficientNGTest.java

@@ -0,0 +1,492 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import java.util.HashMap;
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.UndirectedGraph;
+import org.gephi.graph.api.Node;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Graph;
+import org.gephi.project.api.ProjectController;
+import org.gephi.project.impl.ProjectControllerImpl;
+import org.openide.util.Lookup;
+import static org.testng.Assert.*;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ *
+ * @author akharitonova
+ */
+public class ClusteringCoefficientNGTest {
+    
+    private ProjectController pc;
+    
+    
+    @BeforeClass
+    public void setUp() {
+        pc = Lookup.getDefault().lookup(ProjectControllerImpl.class);
+    }
+
+    @BeforeMethod
+    public void initialize() {
+        pc.newProject();
+    }
+
+    @AfterMethod
+    public void clean() {
+        pc.closeCurrentProject();
+    }
+    
+    @Test
+    public void testOneNodeClusteringCoefficient() {
+        GraphModel graphModel=GraphGenerator.generateCompleteUndirectedGraph(1);
+        Graph hgraph = graphModel.getGraph();
+
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[1];
+        int[] triangles = new int[1];
+        double[] nodeClustering = new double[1];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, false);
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        
+        
+        assertEquals(avClusteringCoefficient, Double.NaN);
+    }
+    
+    @Test
+    public void testTwoConectedNodesClusteringCoefficient() {
+        GraphModel graphModel=GraphGenerator.generateCompleteUndirectedGraph(2);
+        Graph hgraph = graphModel.getGraph();
+
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[2];
+        int[] triangles = new int[2];
+        double[] nodeClustering = new double[2];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, false);
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        
+        
+        assertEquals(avClusteringCoefficient, Double.NaN);
+    }
+    
+    @Test
+    public void testNullGraphClusteringCoefficient() {
+        GraphModel graphModel=GraphGenerator.generateNullUndirectedGraph(5);
+        Graph hgraph = graphModel.getGraph();
+
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[5];
+        int[] triangles = new int[5];
+        double[] nodeClustering = new double[5];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, false);
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        
+        
+        assertEquals(avClusteringCoefficient, Double.NaN);
+    }
+    
+   @Test
+    public void testCompleteGraphClusteringCoefficient() {
+        GraphModel graphModel=GraphGenerator.generateCompleteUndirectedGraph(5);
+        Graph hgraph = graphModel.getGraph();
+
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[5];
+        int[] triangles = new int[5];
+        double[] nodeClustering = new double[5];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, false);
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        
+        assertEquals(avClusteringCoefficient, 1.0);
+    }
+   
+   @Test
+    public void testStarGraphClusteringCoefficient() {
+        GraphModel graphModel=GraphGenerator.generateStarUndirectedGraph(5);
+        Graph hgraph = graphModel.getGraph();
+
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[6];
+        int[] triangles = new int[6];
+        double[] nodeClustering = new double[6];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, false);
+
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        
+        assertEquals(avClusteringCoefficient, 0.0);
+    }
+  
+   
+   @Test
+    public void testSpecial1UndirectedGraphClusteringCoefficient() {
+        GraphModel graphModel=Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph=graphModel.getUndirectedGraph();
+        Node node1=graphModel.factory().newNode("0");
+        Node node2=graphModel.factory().newNode("1");
+        Node node3=graphModel.factory().newNode("2");
+        Node node4=graphModel.factory().newNode("3");
+        Node node5=graphModel.factory().newNode("4");
+        Node node6=graphModel.factory().newNode("5");
+        Node node7=graphModel.factory().newNode("6");
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+        undirectedGraph.addNode(node5);
+        undirectedGraph.addNode(node6);
+        undirectedGraph.addNode(node7);
+        Edge edge12=graphModel.factory().newEdge(node1, node2, false);
+        Edge edge13=graphModel.factory().newEdge(node1, node3, false);
+        Edge edge14=graphModel.factory().newEdge(node1, node4, false);
+        Edge edge15=graphModel.factory().newEdge(node1, node5, false);
+        Edge edge16=graphModel.factory().newEdge(node1, node6, false);
+        Edge edge17=graphModel.factory().newEdge(node1, node7, false);
+        Edge edge23=graphModel.factory().newEdge(node2, node3, false);
+        Edge edge34=graphModel.factory().newEdge(node3, node4, false);
+        Edge edge45=graphModel.factory().newEdge(node4, node5, false);
+        Edge edge56=graphModel.factory().newEdge(node5, node6, false);
+        Edge edge67=graphModel.factory().newEdge(node6, node7, false);
+        Edge edge72=graphModel.factory().newEdge(node7, node2, false);
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge13);
+        undirectedGraph.addEdge(edge14);
+        undirectedGraph.addEdge(edge15);
+        undirectedGraph.addEdge(edge16);
+        undirectedGraph.addEdge(edge17);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge34);
+        undirectedGraph.addEdge(edge45);
+        undirectedGraph.addEdge(edge56);
+        undirectedGraph.addEdge(edge67);
+        undirectedGraph.addEdge(edge72);
+        
+        Graph hgraph = graphModel.getGraph();
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+
+        ArrayWrapper[] network = new ArrayWrapper[7];
+        int[] triangles = new int[7];
+        double[] nodeClustering = new double[7];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, false);
+        
+        double cl1 = nodeClustering[0];
+        double cl3 = nodeClustering[2];
+        
+        double res3=0.667;
+        double diff = 0.01;
+        
+        assertEquals(cl1, 0.4);
+        assertTrue(Math.abs(cl3-res3)<diff);
+        
+    }
+   
+   @Test
+    public void testSpecial2UndirectedGraphClusteringCoefficient() {
+        GraphModel graphModel=Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph=graphModel.getUndirectedGraph();
+        Node node1=graphModel.factory().newNode("0");
+        Node node2=graphModel.factory().newNode("1");
+        Node node3=graphModel.factory().newNode("2");
+        Node node4=graphModel.factory().newNode("3");
+        Node node5=graphModel.factory().newNode("4");
+        Node node6=graphModel.factory().newNode("5");
+        Node node7=graphModel.factory().newNode("6");
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+        undirectedGraph.addNode(node5);
+        undirectedGraph.addNode(node6);
+        undirectedGraph.addNode(node7);
+        Edge edge12=graphModel.factory().newEdge(node1, node2, false);
+        Edge edge23=graphModel.factory().newEdge(node2, node3, false);
+        Edge edge31=graphModel.factory().newEdge(node3, node1, false);
+        Edge edge14=graphModel.factory().newEdge(node1, node4, false);
+        Edge edge45=graphModel.factory().newEdge(node4, node5, false);
+        Edge edge51=graphModel.factory().newEdge(node5, node1, false);
+        Edge edge16=graphModel.factory().newEdge(node1, node6, false);
+        Edge edge67=graphModel.factory().newEdge(node6, node7, false);
+        Edge edge71=graphModel.factory().newEdge(node7, node1, false);
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge31);
+        undirectedGraph.addEdge(edge14);
+        undirectedGraph.addEdge(edge45);
+        undirectedGraph.addEdge(edge51);
+        undirectedGraph.addEdge(edge16);
+        undirectedGraph.addEdge(edge67);
+        undirectedGraph.addEdge(edge71);
+        
+        Graph hgraph = graphModel.getGraph();
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+
+        ArrayWrapper[] network = new ArrayWrapper[7];
+        int[] triangles = new int[7];
+        double[] nodeClustering = new double[7];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, false);
+        
+        double cl2 = nodeClustering[1];
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        
+        double resAv=0.8857;
+        double diff = 0.01;
+        
+        assertEquals(cl2, 1.0);
+        assertTrue(Math.abs(avClusteringCoefficient-resAv)<diff);
+        
+    }
+   
+   @Test
+    public void testSpecial3UndirectedGraphClusteringCoefficient() {
+        GraphModel graphModel=Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph=graphModel.getUndirectedGraph();
+        Node node1=graphModel.factory().newNode("0");
+        Node node2=graphModel.factory().newNode("1");
+        Node node3=graphModel.factory().newNode("2");
+        Node node4=graphModel.factory().newNode("3");
+        Node node5=graphModel.factory().newNode("4");
+        Node node6=graphModel.factory().newNode("5");
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+        undirectedGraph.addNode(node5);
+        undirectedGraph.addNode(node6);
+        Edge edge12=graphModel.factory().newEdge(node1, node2, false);
+        Edge edge23=graphModel.factory().newEdge(node2, node3, false);
+        Edge edge31=graphModel.factory().newEdge(node3, node1, false);
+        Edge edge14=graphModel.factory().newEdge(node1, node4, false);
+        Edge edge25=graphModel.factory().newEdge(node2, node5, false);
+        Edge edge36=graphModel.factory().newEdge(node3, node6, false);
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge31);
+        undirectedGraph.addEdge(edge14);
+        undirectedGraph.addEdge(edge25);
+        undirectedGraph.addEdge(edge36);;
+        
+        Graph hgraph = graphModel.getGraph();
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+
+        ArrayWrapper[] network = new ArrayWrapper[6];
+        int[] triangles = new int[6];
+        double[] nodeClustering = new double[6];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, false);
+        
+        double cl1 = nodeClustering[0];
+        
+        double res1=0.333;
+        double diff = 0.01;
+        
+        assertTrue(Math.abs(cl1-res1)<diff);
+        
+    }
+   
+   @Test
+    public void testTriangleGraphClusteringCoefficient() {
+        GraphModel graphModel=GraphGenerator.generateCompleteUndirectedGraph(3);
+        Graph hgraph = graphModel.getGraph();
+
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[3];
+
+        int[] triangles = new int[3];
+        double[] nodeClustering = new double[3];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, false);
+        
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        
+        assertEquals(avClusteringCoefficient, 1.0);
+    }
+
+   
+   @Test 
+    public void testSpecial1DirectedGraphClusteringCoefficient() {
+        GraphModel graphModel=Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        
+        DirectedGraph directedGraph=graphModel.getDirectedGraph();
+        
+        Node node1=graphModel.factory().newNode("0");
+        Node node2=graphModel.factory().newNode("1");
+        Node node3=graphModel.factory().newNode("2");
+        Node node4=graphModel.factory().newNode("3");
+        
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        
+        Edge edge12=graphModel.factory().newEdge(node1, node2);
+        Edge edge23=graphModel.factory().newEdge(node2, node3);
+        Edge edge24=graphModel.factory().newEdge(node2, node4);
+        Edge edge31=graphModel.factory().newEdge(node3, node1);
+        Edge edge34=graphModel.factory().newEdge(node3, node4);
+        Edge edge41=graphModel.factory().newEdge(node4, node1);
+         
+        directedGraph.addEdge(edge12);
+        directedGraph.addEdge(edge23);
+        directedGraph.addEdge(edge24);
+        directedGraph.addEdge(edge31);
+        directedGraph.addEdge(edge34);
+        directedGraph.addEdge(edge41);
+        
+        
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[4];
+        int[] triangles = new int[4];
+        double[] nodeClustering = new double[4];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, true);
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        
+        
+        assertEquals(avClusteringCoefficient, 0.5);
+    }
+   
+   @Test 
+    public void testTriangleDirectedGraphClusteringCoefficient() {
+        GraphModel graphModel=Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        
+        DirectedGraph directedGraph=graphModel.getDirectedGraph();
+        
+        Node node1=graphModel.factory().newNode("0");
+        Node node2=graphModel.factory().newNode("1");
+        Node node3=graphModel.factory().newNode("2");
+        
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        
+        Edge edge12=graphModel.factory().newEdge(node1, node2);
+        Edge edge21=graphModel.factory().newEdge(node2, node1);
+        Edge edge23=graphModel.factory().newEdge(node2, node3);
+        Edge edge32=graphModel.factory().newEdge(node3, node2);
+        Edge edge31=graphModel.factory().newEdge(node3, node1);
+        Edge edge13=graphModel.factory().newEdge(node1, node3);
+         
+        directedGraph.addEdge(edge12);
+        directedGraph.addEdge(edge21);
+        directedGraph.addEdge(edge23);
+        directedGraph.addEdge(edge32);
+        directedGraph.addEdge(edge31);
+        directedGraph.addEdge(edge13);
+        
+        
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[3];
+        int[] triangles = new int[3];
+        double[] nodeClustering = new double[3];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, true);
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        
+        
+        assertEquals(avClusteringCoefficient, 1.);
+    }
+   
+   @Test 
+    public void testSpecial2DirectedGraphClusteringCoefficient() {
+        GraphModel graphModel=Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        
+        DirectedGraph directedGraph=graphModel.getDirectedGraph();
+        
+        Node node1=graphModel.factory().newNode("0");
+        Node node2=graphModel.factory().newNode("1");
+        Node node3=graphModel.factory().newNode("2");
+        Node node4=graphModel.factory().newNode("3");
+        
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        
+        Edge edge21=graphModel.factory().newEdge(node2, node1);
+        Edge edge24=graphModel.factory().newEdge(node2, node4);
+        Edge edge31=graphModel.factory().newEdge(node3, node1);
+        Edge edge32=graphModel.factory().newEdge(node3, node2);
+        Edge edge43=graphModel.factory().newEdge(node4, node3);
+         
+        directedGraph.addEdge(edge21);
+        directedGraph.addEdge(edge24);
+        directedGraph.addEdge(edge31);
+        directedGraph.addEdge(edge32);
+        directedGraph.addEdge(edge43);
+        
+        
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[4];
+        int[] triangles = new int[4];
+        double[] nodeClustering = new double[4];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, true);
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        double res = 0.4167;
+        double diff = 0.01;
+        
+        assertTrue(Math.abs(avClusteringCoefficient-res)<diff);
+    }
+   
+    @Test 
+    public void testTriangleNonCompleteDirectedGraphClusteringCoefficient() {
+        GraphModel graphModel=Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        
+        DirectedGraph directedGraph=graphModel.getDirectedGraph();
+        
+        Node node1=graphModel.factory().newNode("0");
+        Node node2=graphModel.factory().newNode("1");
+        Node node3=graphModel.factory().newNode("2");
+        
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        
+        Edge edge12=graphModel.factory().newEdge(node1, node2);
+        Edge edge21=graphModel.factory().newEdge(node2, node1);
+        Edge edge23=graphModel.factory().newEdge(node2, node3);
+        Edge edge32=graphModel.factory().newEdge(node3, node2);
+        Edge edge13=graphModel.factory().newEdge(node1, node3);
+         
+        directedGraph.addEdge(edge12);
+        directedGraph.addEdge(edge21);
+        directedGraph.addEdge(edge23);
+        directedGraph.addEdge(edge32);
+        directedGraph.addEdge(edge13);
+        
+        
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        
+        ClusteringCoefficient cc = new ClusteringCoefficient();
+        ArrayWrapper[] network = new ArrayWrapper[3];
+        int[] triangles = new int[3];
+        double[] nodeClustering = new double[3];
+
+        HashMap<String, Double> results = cc.computeClusteringCoefficient(hgraph, network, triangles, nodeClustering, true);
+        double avClusteringCoefficient = results.get("clusteringCoefficient");
+        double res = 0.833;
+        double diff = 0.01;
+        
+        assertTrue(Math.abs(avClusteringCoefficient-res)<diff);
+    }
+}

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/ConnectedComponentsNGTest.java

@@ -0,0 +1,451 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import java.util.HashMap;
+import java.util.LinkedList;
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.graph.api.UndirectedGraph;
+import org.gephi.project.api.ProjectController;
+import org.gephi.project.impl.ProjectControllerImpl;
+import org.openide.util.Lookup;
+import static org.testng.Assert.*;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ *
+ * @author Anna
+ */
+public class ConnectedComponentsNGTest {
+
+    private ProjectController pc;
+
+    @BeforeClass
+    public void setUp() {
+        pc = Lookup.getDefault().lookup(ProjectControllerImpl.class);
+    }
+
+    @BeforeMethod
+    public void initialize() {
+        pc.newProject();
+    }
+
+    @AfterMethod
+    public void clean() {
+        pc.closeCurrentProject();
+    }
+
+    @Test
+    public void testComputeOneNodeWeeklyConnectedComponents() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(1);
+        UndirectedGraph graph = graphModel.getUndirectedGraph();
+        Node n = graph.getNode("0");
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
+        indicies.put(n, 0);
+        LinkedList<LinkedList<Node>> components = c.computeWeeklyConnectedComponents(graph, indicies);
+        assertEquals(components.size(), 1);
+    }
+
+    @Test
+    public void testNullGraphWeeklyConnectedComponents() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
+        UndirectedGraph graph = graphModel.getUndirectedGraph();
+        Node n0 = graph.getNode("0");
+        Node n1 = graph.getNode("1");
+        Node n2 = graph.getNode("2");
+        Node n3 = graph.getNode("3");
+        Node n4 = graph.getNode("4");
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
+        indicies.put(n0, 0);
+        indicies.put(n1, 1);
+        indicies.put(n2, 2);
+        indicies.put(n3, 3);
+        indicies.put(n4, 4);
+        LinkedList<LinkedList<Node>> components = c.computeWeeklyConnectedComponents(graph, indicies);
+        assertEquals(components.size(), 5);
+    }
+
+    @Test
+    public void testComputeBarbellGraphWeeklyConnectedComponents() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node[] nodes = new Node[4];
+        for (int i = 0; i < 4; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
+            nodes[i] = currentNode;
+            undirectedGraph.addNode(currentNode);
+        }
+        for (int i = 0; i < 3; i++) {
+            for (int j = i + 1; j < 4; j++) {
+                Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
+                undirectedGraph.addEdge(currentEdge);
+            }
+        }
+        Edge currentEdge = graphModel.factory().newEdge(undirectedGraph.getNode("0"), undirectedGraph.getNode("5"), false);
+        undirectedGraph.addEdge(currentEdge);
+        UndirectedGraph graph = graphModel.getUndirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> components = c.computeWeeklyConnectedComponents(graph, indicies);
+        assertEquals(components.size(), 1);
+    }
+
+    @Test
+    public void testSpecial1UndirectedGraphConnectedComponents() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+        undirectedGraph.addNode(node5);
+        Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
+        Edge edge14 = graphModel.factory().newEdge(node1, node4, false);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
+        Edge edge25 = graphModel.factory().newEdge(node2, node5, false);
+        Edge edge35 = graphModel.factory().newEdge(node3, node5, false);
+        Edge edge43 = graphModel.factory().newEdge(node4, node3, false);
+        Edge edge51 = graphModel.factory().newEdge(node5, node1, false);
+        Edge edge54 = graphModel.factory().newEdge(node5, node4, false);
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge14);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge25);
+        undirectedGraph.addEdge(edge35);
+        undirectedGraph.addEdge(edge43);
+        undirectedGraph.addEdge(edge51);
+        undirectedGraph.addEdge(edge54);
+
+        UndirectedGraph graph = graphModel.getUndirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> components = c.computeWeeklyConnectedComponents(graph, indicies);
+        assertEquals(components.size(), 1);
+    }
+
+    @Test
+    public void testSpecial2UndirectedGraphConnectedComponents() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        Node node6 = graphModel.factory().newNode("5");
+        Node node7 = graphModel.factory().newNode("6");
+        Node node8 = graphModel.factory().newNode("7");
+        Node node9 = graphModel.factory().newNode("8");
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+        undirectedGraph.addNode(node5);
+        undirectedGraph.addNode(node6);
+        undirectedGraph.addNode(node7);
+        undirectedGraph.addNode(node8);
+        undirectedGraph.addNode(node9);
+        Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
+        Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
+        Edge edge56 = graphModel.factory().newEdge(node5, node6, false);
+        Edge edge64 = graphModel.factory().newEdge(node6, node4, false);
+        Edge edge75 = graphModel.factory().newEdge(node7, node5, false);
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge45);
+        undirectedGraph.addEdge(edge56);
+        undirectedGraph.addEdge(edge64);
+        undirectedGraph.addEdge(edge75);
+
+        UndirectedGraph graph = graphModel.getUndirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> components = c.computeWeeklyConnectedComponents(graph, indicies);
+
+        int componentNumber3 = c.getComponentNumber(components, node3);
+        int componentNumber4 = c.getComponentNumber(components, node4);
+        int componentNumber7 = c.getComponentNumber(components, node7);
+        int componentNumber8 = c.getComponentNumber(components, node8);
+
+        assertEquals(components.size(), 4);
+        assertEquals(componentNumber4, componentNumber7);
+        assertNotEquals(componentNumber3, componentNumber8);
+    }
+
+    @Test
+    public void testDirectedPathGraphConnectedComponents() {
+        GraphModel graphModel = GraphGenerator.generatePathDirectedGraph(4);
+        DirectedGraph graph = graphModel.getDirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> components = c.top_tarjans(graph, indicies);
+        assertEquals(components.size(), 4);
+    }
+
+    @Test
+    public void testDirectedCyclicGraphConnectedComponents() {
+        GraphModel graphModel = GraphGenerator.generateCyclicDirectedGraph(5);
+        DirectedGraph graph = graphModel.getDirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> components = c.top_tarjans(graph, indicies);
+        assertEquals(components.size(), 1);
+    }
+
+    @Test
+    public void testSpecial1DirectedGraphConnectedComponents() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        directedGraph.addNode(node5);
+        Edge edge12 = graphModel.factory().newEdge(node1, node2);
+        Edge edge14 = graphModel.factory().newEdge(node1, node4);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3);
+        Edge edge25 = graphModel.factory().newEdge(node2, node5);
+        Edge edge35 = graphModel.factory().newEdge(node3, node5);
+        Edge edge43 = graphModel.factory().newEdge(node4, node3);
+        Edge edge51 = graphModel.factory().newEdge(node5, node1);
+        Edge edge54 = graphModel.factory().newEdge(node5, node4);
+        directedGraph.addEdge(edge12);
+        directedGraph.addEdge(edge14);
+        directedGraph.addEdge(edge23);
+        directedGraph.addEdge(edge25);
+        directedGraph.addEdge(edge35);
+        directedGraph.addEdge(edge43);
+        directedGraph.addEdge(edge51);
+        directedGraph.addEdge(edge54);
+
+        DirectedGraph graph = graphModel.getDirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> components = c.top_tarjans(graph, indicies);
+        assertEquals(components.size(), 1);
+    }
+
+    @Test
+    public void testSpecial2DirectedGraphConnectedComponents() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        directedGraph.addNode(node5);
+        Edge edge12 = graphModel.factory().newEdge(node1, node2);
+        Edge edge14 = graphModel.factory().newEdge(node1, node4);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3);
+        Edge edge25 = graphModel.factory().newEdge(node2, node5);
+        Edge edge35 = graphModel.factory().newEdge(node3, node5);
+        Edge edge43 = graphModel.factory().newEdge(node4, node3);
+        Edge edge54 = graphModel.factory().newEdge(node5, node4);
+        directedGraph.addEdge(edge12);
+        directedGraph.addEdge(edge14);
+        directedGraph.addEdge(edge23);
+        directedGraph.addEdge(edge25);
+        directedGraph.addEdge(edge35);
+        directedGraph.addEdge(edge43);
+        directedGraph.addEdge(edge54);
+
+        DirectedGraph graph = graphModel.getDirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> weeklyConnectedComponents = c.computeWeeklyConnectedComponents(graph, indicies);
+        LinkedList<LinkedList<Node>> stronglyConnectedComponents = c.top_tarjans(graph, indicies);
+        int componentNumber1 = c.getComponentNumber(stronglyConnectedComponents, node1);
+        int componentNumber3 = c.getComponentNumber(stronglyConnectedComponents, node3);
+        int componentNumber4 = c.getComponentNumber(stronglyConnectedComponents, node4);
+        int componentNumber5 = c.getComponentNumber(stronglyConnectedComponents, node5);
+
+        assertEquals(stronglyConnectedComponents.size(), 3);
+        assertEquals(weeklyConnectedComponents.size(), 1);
+        assertEquals(componentNumber3, componentNumber5);
+        assertNotEquals(componentNumber1, componentNumber4);
+    }
+
+    @Test
+    public void testSpecial3DirectedGraphConnectedComponents() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        Node node6 = graphModel.factory().newNode("5");
+        Node node7 = graphModel.factory().newNode("6");
+        Node node8 = graphModel.factory().newNode("7");
+        Node node9 = graphModel.factory().newNode("8");
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        directedGraph.addNode(node5);
+        directedGraph.addNode(node6);
+        directedGraph.addNode(node7);
+        directedGraph.addNode(node8);
+        directedGraph.addNode(node9);
+        Edge edge12 = graphModel.factory().newEdge(node1, node2);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3);
+        Edge edge45 = graphModel.factory().newEdge(node4, node5);
+        Edge edge56 = graphModel.factory().newEdge(node5, node6);
+        Edge edge64 = graphModel.factory().newEdge(node6, node4);
+        Edge edge75 = graphModel.factory().newEdge(node7, node5);
+        Edge edge89 = graphModel.factory().newEdge(node8, node9);
+        Edge edge98 = graphModel.factory().newEdge(node9, node8);
+        directedGraph.addEdge(edge12);
+        directedGraph.addEdge(edge23);
+        directedGraph.addEdge(edge45);
+        directedGraph.addEdge(edge56);
+        directedGraph.addEdge(edge64);
+        directedGraph.addEdge(edge75);
+        directedGraph.addEdge(edge89);
+        directedGraph.addEdge(edge98);
+
+        DirectedGraph graph = graphModel.getDirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> stronglyConnectedComponents = c.top_tarjans(graph, indicies);
+
+        assertEquals(stronglyConnectedComponents.size(), 6);
+    }
+
+    @Test
+    public void testSpecial4DirectedGraphConnectedComponents() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        Node node6 = graphModel.factory().newNode("5");
+        Node node7 = graphModel.factory().newNode("6");
+        Node node8 = graphModel.factory().newNode("7");
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        directedGraph.addNode(node5);
+        directedGraph.addNode(node6);
+        directedGraph.addNode(node7);
+        directedGraph.addNode(node8);
+        Edge edge12 = graphModel.factory().newEdge(node1, node2);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3);
+        Edge edge34 = graphModel.factory().newEdge(node3, node4);
+        Edge edge41 = graphModel.factory().newEdge(node4, node1);
+        Edge edge56 = graphModel.factory().newEdge(node5, node6);
+        Edge edge67 = graphModel.factory().newEdge(node6, node7);
+        Edge edge78 = graphModel.factory().newEdge(node7, node8);
+        Edge edge85 = graphModel.factory().newEdge(node8, node5);
+        Edge edge45 = graphModel.factory().newEdge(node4, node5);
+        directedGraph.addEdge(edge12);
+        directedGraph.addEdge(edge23);
+        directedGraph.addEdge(edge34);
+        directedGraph.addEdge(edge41);
+        directedGraph.addEdge(edge56);
+        directedGraph.addEdge(edge67);
+        directedGraph.addEdge(edge78);
+        directedGraph.addEdge(edge85);
+        directedGraph.addEdge(edge45);
+
+        DirectedGraph graph = graphModel.getDirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> stronglyConnectedComponents = c.top_tarjans(graph, indicies);
+
+        int componentNumber1 = c.getComponentNumber(stronglyConnectedComponents, node1);
+        int componentNumber5 = c.getComponentNumber(stronglyConnectedComponents, node5);
+
+        assertEquals(stronglyConnectedComponents.size(), 2);
+        assertNotEquals(componentNumber1, componentNumber5);
+    }
+
+    @Test
+    public void testSpecial2UndirectedGraphGiantComponent() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        Node node6 = graphModel.factory().newNode("5");
+        Node node7 = graphModel.factory().newNode("6");
+        Node node8 = graphModel.factory().newNode("7");
+        Node node9 = graphModel.factory().newNode("8");
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+        undirectedGraph.addNode(node5);
+        undirectedGraph.addNode(node6);
+        undirectedGraph.addNode(node7);
+        undirectedGraph.addNode(node8);
+        undirectedGraph.addNode(node9);
+        Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
+        Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
+        Edge edge56 = graphModel.factory().newEdge(node5, node6, false);
+        Edge edge64 = graphModel.factory().newEdge(node6, node4, false);
+        Edge edge75 = graphModel.factory().newEdge(node7, node5, false);
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge45);
+        undirectedGraph.addEdge(edge56);
+        undirectedGraph.addEdge(edge64);
+        undirectedGraph.addEdge(edge75);
+
+        UndirectedGraph graph = graphModel.getUndirectedGraph();
+
+        ConnectedComponents c = new ConnectedComponents();
+        HashMap<Node, Integer> indicies = c.createIndiciesMap(graph);
+        LinkedList<LinkedList<Node>> components = c.computeWeeklyConnectedComponents(graph, indicies);
+        c.fillComponentSizeList(components);
+
+        int giantComponent = c.getGiantComponent();
+        int componentNumber5 = c.getComponentNumber(components, node5);
+
+        assertEquals(giantComponent, componentNumber5);
+    }
+}

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/DegreeNGTest.java

@@ -0,0 +1,168 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.project.api.ProjectController;
+import org.gephi.project.impl.ProjectControllerImpl;
+import org.openide.util.Lookup;
+import static org.testng.Assert.*;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ *
+ * @author Anna
+ */
+public class DegreeNGTest {
+
+    private ProjectController pc;
+
+    @BeforeClass
+    public void setUp() {
+        pc = Lookup.getDefault().lookup(ProjectControllerImpl.class);
+    }
+
+    @BeforeMethod
+    public void initialize() {
+        pc.newProject();
+    }
+
+    @AfterMethod
+    public void clean() {
+        pc.closeCurrentProject();
+    }
+
+    @Test
+    public void testOneNodeDegree() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(1);
+        Graph graph = graphModel.getGraph();
+        Node n = graph.getNode("0");
+
+        Degree d = new Degree();
+        int degree = d.calculateDegree(graph, n);
+        assertEquals(degree, 0);
+    }
+
+    @Test
+    public void testNullGraphDegree() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
+        Graph graph = graphModel.getGraph();
+        Node n = graph.getNode("1");
+        Degree d = new Degree();
+        int degree = d.calculateDegree(graph, n);
+        double avDegree = d.calculateAverageDegree(graph, false, false);
+        assertEquals(degree, 0);
+        assertEquals(avDegree, 0.0);
+    }
+
+    @Test
+    public void testCompleteGraphDegree() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(5);
+        Graph graph = graphModel.getGraph();
+        Node n = graph.getNode("2");
+        Degree d = new Degree();
+        int degree = d.calculateDegree(graph, n);
+        assertEquals(degree, 4);
+    }
+
+    @Test
+    public void testStarGraphDegree() {
+        GraphModel graphModel = GraphGenerator.generateStarUndirectedGraph(5);
+        Graph graph = graphModel.getGraph();
+        Node n1 = graph.getNode("0");
+        Node n2 = graph.getNode("1");
+        Degree d = new Degree();
+        int degree1 = d.calculateDegree(graph, n1);
+        int degree2 = d.calculateDegree(graph, n2);
+        double avDegree = d.calculateAverageDegree(graph, false, false);
+        double expectedAvDegree = 1.6667;
+        double diff = Math.abs(avDegree - expectedAvDegree);
+        assertEquals(degree1, 5);
+        assertEquals(degree2, 1);
+        assertTrue(diff < 0.001);
+    }
+
+    @Test
+    public void testCyclicGraphDegree() {
+        GraphModel graphModel = GraphGenerator.generateCyclicUndirectedGraph(5);
+        Graph graph = graphModel.getGraph();
+        Node n = graph.getNode("3");
+        Degree d = new Degree();
+        int degree = d.calculateDegree(graph, n);
+        double avDegree = d.calculateAverageDegree(graph, false, false);
+        assertEquals(degree, 2);
+        assertEquals(avDegree, 2.0);
+    }
+
+    @Test
+    public void testDirectedPathGraphDegree() {
+        GraphModel graphModel = GraphGenerator.generatePathDirectedGraph(2);
+        DirectedGraph graph = graphModel.getDirectedGraph();
+        Node n1 = graph.getNode("0");
+        Node n2 = graph.getNode("1");
+        Degree d = new Degree();
+        int inDegree1 = d.calculateInDegree(graph, n1);
+        int inDegree2 = d.calculateInDegree(graph, n2);
+        int outDegree1 = d.calculateOutDegree(graph, n1);
+        double avDegree = d.calculateAverageDegree(graph, true, false);
+        assertEquals(inDegree1, 0);
+        assertEquals(inDegree2, 1);
+        assertEquals(outDegree1, 1);
+        assertEquals(avDegree, 1.0);
+    }
+
+    @Test
+    public void testDirectedCyclicGraphDegree() {
+        GraphModel graphModel = GraphGenerator.generateCyclicDirectedGraph(5);
+        DirectedGraph graph = graphModel.getDirectedGraph();
+        Node n1 = graph.getNode("0");
+        Node n3 = graph.getNode("2");
+        Node n5 = graph.getNode("4");
+        Degree d = new Degree();
+        int inDegree3 = d.calculateInDegree(graph, n3);
+        int degree1 = d.calculateDegree(graph, n1);
+        int outDegree5 = d.calculateOutDegree(graph, n5);
+        double avDegree = d.calculateAverageDegree(graph, true, false);
+        assertEquals(inDegree3, 1);
+        assertEquals(degree1, 2);
+        assertEquals(outDegree5, 1);
+        assertEquals(avDegree, 2.0);
+    }
+
+    @Test
+    public void testDirectedStarOutGraphDegree() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node firstNode = graphModel.factory().newNode("0");
+        directedGraph.addNode(firstNode);
+        for (int i = 1; i <= 5; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            directedGraph.addNode(currentNode);
+            Edge currentEdge = graphModel.factory().newEdge(firstNode, currentNode);
+            directedGraph.addEdge(currentEdge);
+        }
+
+        DirectedGraph graph = graphModel.getDirectedGraph();
+        Node n1 = graph.getNode("0");
+        Node n3 = graph.getNode("2");
+        Degree d = new Degree();
+        int inDegree1 = d.calculateInDegree(graph, n1);
+        int outDegree1 = d.calculateOutDegree(graph, n1);
+        int degree3 = d.calculateDegree(graph, n3);
+
+        assertEquals(inDegree1, 0);
+        assertEquals(outDegree1, 5);
+        assertEquals(degree3, 1);
+    }
+}

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/EdgeWrapperNGTest.java

@@ -0,0 +1,22 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import static org.testng.Assert.*;
+import org.testng.annotations.Test;
+
+/**
+ *
+ * @author Anna
+ */
+public class EdgeWrapperNGTest {
+    
+    public EdgeWrapperNGTest() {
+    }
+
+    @Test
+    public void testSomeMethod() {
+    }
+}

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/EigenvectorCentralityNGTest.java

@@ -0,0 +1,437 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import java.util.HashMap;
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.graph.api.UndirectedGraph;
+import org.gephi.project.api.ProjectController;
+import org.gephi.project.impl.ProjectControllerImpl;
+import org.openide.util.Lookup;
+import static org.testng.Assert.*;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ *
+ * @author Anna
+ */
+public class EigenvectorCentralityNGTest {
+
+    private ProjectController pc;
+
+    @BeforeClass
+    public void setUp() {
+        pc = Lookup.getDefault().lookup(ProjectControllerImpl.class);
+    }
+
+    @BeforeMethod
+    public void initialize() {
+        pc.newProject();
+    }
+
+    @AfterMethod
+    public void clean() {
+        pc.closeCurrentProject();
+    }
+
+    @Test
+    public void testOneNodeEigenvectorCentrality() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(1);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[1];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);
+
+        Node n1 = hgraph.getNode("0");
+        int index = invIndicies.get(n1);
+        double ec1 = centralities[index];
+
+        assertEquals(ec1, 0.0);
+    }
+
+    @Test
+    public void testTwoConnectedNodesEigenvectorCentrality() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(2);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[2];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);
+
+        Node n1 = hgraph.getNode("0");
+        int index = invIndicies.get(n1);
+        double ec1 = centralities[index];
+
+        assertEquals(ec1, 1.0);
+    }
+
+    @Test
+    public void testNullGraphEigenvectorCentrality() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[5];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);
+
+        Node n2 = hgraph.getNode("1");
+        int index = invIndicies.get(n2);
+        double ec2 = centralities[index];
+
+        assertEquals(ec2, 0.0);
+    }
+
+    @Test
+    public void testCompleteUndirectedGraphEigenvectorCentrality() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(5);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[5];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);
+
+        Node n1 = hgraph.getNode("0");
+        Node n3 = hgraph.getNode("2");
+        int index1 = invIndicies.get(n1);
+        int index3 = invIndicies.get(n3);
+        double ec1 = centralities[index1];
+        double ec3 = centralities[index3];
+
+        assertEquals(ec1, 1.0);
+        assertEquals(ec3, 1.0);
+    }
+
+    @Test
+    public void testSpecial1UndirectedGraphEigenvectorCentrlity() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+
+        Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
+        Edge edge34 = graphModel.factory().newEdge(node3, node4, false);
+        Edge edge13 = graphModel.factory().newEdge(node1, node3, false);
+        Edge edge24 = graphModel.factory().newEdge(node2, node4, false);
+
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge34);
+        undirectedGraph.addEdge(edge13);
+        undirectedGraph.addEdge(edge24);
+
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[4];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);
+
+        int index1 = invIndicies.get(node1);
+        int index2 = invIndicies.get(node2);
+        int index3 = invIndicies.get(node3);
+        double ec1 = centralities[index1];
+        double ec2 = centralities[index2];
+        double ec3 = centralities[index3];
+
+        assertEquals(ec2, ec3);
+        assertNotEquals(ec1, ec2);
+        assertEquals(ec3, 1.0);
+    }
+
+    @Test
+    public void testSpecial2UndirectedGraphEigenvectorCentrlity() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+        undirectedGraph.addNode(node5);
+
+        Edge edge13 = graphModel.factory().newEdge(node1, node3, false);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
+        Edge edge34 = graphModel.factory().newEdge(node3, node4, false);
+        Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
+
+        undirectedGraph.addEdge(edge13);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge34);
+        undirectedGraph.addEdge(edge45);
+
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[5];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);
+
+        int index2 = invIndicies.get(node2);
+        int index3 = invIndicies.get(node3);
+        int index4 = invIndicies.get(node4);
+        double ec2 = centralities[index2];
+        double ec3 = centralities[index3];
+        double ec4 = centralities[index4];
+
+        double res = 0.765;
+        double diff = 0.01;
+
+        assertTrue(ec2 < ec3);
+        assertTrue(Math.abs(ec4 - res) < diff);
+    }
+
+    @Test
+    public void testSpecial3UndirectedGraphEigenvectorCentrlity() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+
+        Edge edge11 = graphModel.factory().newEdge(node1, node1, false);
+        Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
+        Edge edge33 = graphModel.factory().newEdge(node3, node3, false);
+
+        undirectedGraph.addEdge(edge11);
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge33);
+
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[3];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, false, 100);
+
+        int index1 = invIndicies.get(node1);
+        int index2 = invIndicies.get(node2);
+        double ec1 = centralities[index1];
+        double ec2 = centralities[index2];
+
+        assertEquals(ec1, ec2);
+    }
+
+    @Test
+    public void testCyclicDirectedGraphEigenvectorCentrality() {
+        GraphModel graphModel = GraphGenerator.generateCyclicDirectedGraph(3);
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[3];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, true, 100);
+
+        Node n1 = hgraph.getNode("0");
+        int index1 = invIndicies.get(n1);
+        double ec1 = centralities[index1];
+
+        assertEquals(ec1, 1.0);
+    }
+
+    @Test
+    public void testSpecial1DirectedEigenvectorCentrality() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        directedGraph.addNode(node5);
+
+        Edge edge12 = graphModel.factory().newEdge(node1, node2);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3);
+        Edge edge31 = graphModel.factory().newEdge(node3, node1);
+        Edge edge42 = graphModel.factory().newEdge(node4, node2);
+        Edge edge54 = graphModel.factory().newEdge(node5, node4);
+
+        directedGraph.addEdge(edge12);
+        directedGraph.addEdge(edge23);
+        directedGraph.addEdge(edge31);
+        directedGraph.addEdge(edge42);
+        directedGraph.addEdge(edge54);
+
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[5];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, true, 1000);
+
+        int index1 = invIndicies.get(node1);
+        int index2 = invIndicies.get(node2);
+        int index4 = invIndicies.get(node4);
+        int index5 = invIndicies.get(node5);
+
+        double ec1 = centralities[index1];
+        double ec2 = centralities[index2];
+        double ec4 = centralities[index4];
+        double ec5 = centralities[index5];
+
+        double diff = 0.01;
+        double res0 = 0.;
+        double res1 = 1.;
+
+        assertEquals(ec5, 0.0);
+        assertTrue(Math.abs(ec4 - res0) < diff);
+        assertTrue(Math.abs(ec1 - res1) < diff);
+        assertTrue(Math.abs(ec1 - ec2) < diff);
+    }
+
+    @Test
+    public void testDirectedStarOutEigenvectorCentrality() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node firstNode = graphModel.factory().newNode("0");
+        directedGraph.addNode(firstNode);
+        for (int i = 1; i <= 5; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            directedGraph.addNode(currentNode);
+            Edge currentEdge = graphModel.factory().newEdge(firstNode, currentNode);
+            directedGraph.addEdge(currentEdge);
+        }
+
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[6];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, true, 100);
+
+        Node n1 = hgraph.getNode("0");
+        Node n2 = hgraph.getNode("1");
+        int index1 = invIndicies.get(n1);
+        int index2 = invIndicies.get(n2);
+        double ec1 = centralities[index1];
+        double ec2 = centralities[index2];
+
+        assertEquals(ec1, 0.0);
+        assertEquals(ec2, 1.0);
+    }
+
+    @Test
+    public void testPathDirectedGraphEigenvectorCentrality() {
+        GraphModel graphModel = GraphGenerator.generatePathDirectedGraph(4);
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+
+        EigenvectorCentrality ec = new EigenvectorCentrality();
+
+        double[] centralities = new double[4];
+
+        HashMap<Integer, Node> indicies = new HashMap();
+        HashMap<Node, Integer> invIndicies = new HashMap();
+
+        ec.fillIndiciesMaps(hgraph, centralities, indicies, invIndicies);
+
+        ec.calculateEigenvectorCentrality(hgraph, centralities, indicies, invIndicies, true, 100);
+
+        Node n1 = hgraph.getNode("0");
+        Node n4 = hgraph.getNode("3");
+        int index1 = invIndicies.get(n1);
+        int index4 = invIndicies.get(n4);
+        double ec1 = centralities[index1];
+        double ec4 = centralities[index4];
+
+        assertEquals(ec1, 0.0);
+        assertEquals(ec4, 1.0);
+    }
+}

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/GraphDensityNGTest.java

@@ -0,0 +1,195 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.graph.api.UndirectedGraph;
+import org.gephi.project.api.ProjectController;
+import org.gephi.project.impl.ProjectControllerImpl;
+import org.openide.util.Lookup;
+import static org.testng.Assert.*;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ *
+ * @author Anna
+ */
+public class GraphDensityNGTest {
+
+    private ProjectController pc;
+
+    @BeforeClass
+    public void setUp() {
+        pc = Lookup.getDefault().lookup(ProjectControllerImpl.class);
+    }
+
+    @BeforeMethod
+    public void initialize() {
+        pc.newProject();
+    }
+
+    @AfterMethod
+    public void clean() {
+        pc.closeCurrentProject();
+    }
+
+    @Test
+    public void testOneNodeDensity() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(1);
+        Graph graph = graphModel.getGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, false);
+        assertEquals(density, Double.NaN);
+    }
+
+    @Test
+    public void testTwoConnectedNodesDensity() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(2);
+        Graph graph = graphModel.getGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, false);
+        assertEquals(density, 1.0);
+    }
+
+    @Test
+    public void testNullGraphDensity() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
+        Graph graph = graphModel.getGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, false);
+        assertEquals(density, 0.0);
+    }
+
+    @Test
+    public void testCompleteGraphDensity() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(5);
+        Graph graph = graphModel.getGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, false);
+        assertEquals(density, 1.0);
+    }
+
+    @Test
+    public void testCyclicGraphDensity() {
+        GraphModel graphModel = GraphGenerator.generateCyclicUndirectedGraph(6);
+        Graph graph = graphModel.getGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, false);
+        assertEquals(density, 0.4);
+    }
+
+    @Test
+    public void testSelfLoopNodeDensity() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node currentNode = graphModel.factory().newNode("0");
+        undirectedGraph.addNode(currentNode);
+        Edge currentEdge = graphModel.factory().newEdge(currentNode, currentNode, false);
+        undirectedGraph.addEdge(currentEdge);
+        Graph graph = graphModel.getGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, false);
+        assertEquals(density, Double.POSITIVE_INFINITY);
+    }
+
+    @Test
+    public void testCompleteGraphWithSelfLoopsDensity() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(3);
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node n1 = undirectedGraph.getNode("0");
+        Node n2 = undirectedGraph.getNode("1");
+        Node n3 = undirectedGraph.getNode("2");
+        Edge currentEdge = graphModel.factory().newEdge(n1, n1, false);
+        undirectedGraph.addEdge(currentEdge);
+        currentEdge = graphModel.factory().newEdge(n2, n2, false);
+        undirectedGraph.addEdge(currentEdge);
+        currentEdge = graphModel.factory().newEdge(n3, n3, false);
+        undirectedGraph.addEdge(currentEdge);
+        Graph graph = graphModel.getGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, false);
+        assertEquals(density, 2.0);
+    }
+
+    @Test
+    public void testTwoCompleteGraphsDensity() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node[] nodes = new Node[4];
+        for (int i = 0; i < 4; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
+            nodes[i] = currentNode;
+            undirectedGraph.addNode(currentNode);
+        }
+        for (int i = 0; i < 3; i++) {
+            for (int j = i + 1; j < 4; j++) {
+                Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
+                undirectedGraph.addEdge(currentEdge);
+            }
+        }
+        Graph graph = graphModel.getGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, false);
+        double expectedAvDegree = 0.4286;
+        double diff = Math.abs(density - expectedAvDegree);
+        assertTrue(diff < 0.01);
+    }
+
+    @Test
+    public void testDirectedPathGraphDensity() {
+        GraphModel graphModel = GraphGenerator.generatePathDirectedGraph(2);
+        DirectedGraph graph = graphModel.getDirectedGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, true);
+        assertEquals(density, 0.5);
+    }
+
+    @Test
+    public void testDirectedCyclicGraphDensity() {
+        GraphModel graphModel = GraphGenerator.generateCyclicDirectedGraph(5);
+        DirectedGraph graph = graphModel.getDirectedGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, true);
+        assertEquals(density, 0.25);
+    }
+
+    @Test
+    public void testDirectedCompleteGraphDensity() {
+        GraphModel graphModel = GraphGenerator.generateCompleteDirectedGraph(5);
+        DirectedGraph graph = graphModel.getDirectedGraph();
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, true);
+        assertEquals(density, 1.0);
+    }
+
+    @Test
+    public void testDirectedCompleteGraphWithSelfLoopsDensity() {
+        GraphModel graphModel = GraphGenerator.generateCompleteDirectedGraph(3);
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node n1 = directedGraph.getNode("0");
+        Node n2 = directedGraph.getNode("1");
+        Node n3 = directedGraph.getNode("2");
+        Edge currentEdge = graphModel.factory().newEdge(n1, n1);
+        directedGraph.addEdge(currentEdge);
+        currentEdge = graphModel.factory().newEdge(n2, n2);
+        directedGraph.addEdge(currentEdge);
+        currentEdge = graphModel.factory().newEdge(n3, n3);
+        directedGraph.addEdge(currentEdge);
+
+        DirectedGraph graph = graphModel.getDirectedGraph();
+
+        GraphDensity d = new GraphDensity();
+        double density = d.calculateDensity(graph, true);
+        assertEquals(density, 1.5);
+    }
+}

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/GraphGenerator.java

@@ -0,0 +1,174 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.graph.api.UndirectedGraph;
+import org.openide.util.Lookup;
+
+/**
+ *
+ * @author mbastian
+ */
+public class GraphGenerator {
+
+    public static GraphModel generateNullUndirectedGraph(int n) {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        for (int i = 0; i < n; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            undirectedGraph.addNode(currentNode);
+        }
+        return graphModel;
+    }
+
+    public static GraphModel generateCompleteUndirectedGraph(int n) {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node[] nodes = new Node[n];
+        for (int i = 0; i < n; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            nodes[i] = currentNode;
+            undirectedGraph.addNode(currentNode);
+        }
+        for (int i = 0; i < n - 1; i++) {
+            for (int j = i + 1; j < n; j++) {
+                Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
+                undirectedGraph.addEdge(currentEdge);
+            }
+        }
+        return graphModel;
+    }
+
+    public static GraphModel generatePathUndirectedGraph(int n) {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        if (n <= 0) {
+            return graphModel;
+        }
+        Node firstNode = graphModel.factory().newNode("0");
+        undirectedGraph.addNode(firstNode);
+        Node prevNode = firstNode;
+        for (int i = 1; i < n; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            undirectedGraph.addNode(currentNode);
+            Edge currentEdge = graphModel.factory().newEdge(prevNode, currentNode, false);
+            undirectedGraph.addEdge(currentEdge);
+            prevNode = currentNode;
+        }
+        return graphModel;
+    }
+
+    public static GraphModel generateCyclicUndirectedGraph(int n) {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        if (n <= 0) {
+            return graphModel;
+        }
+        Node firstNode = graphModel.factory().newNode("0");
+        undirectedGraph.addNode(firstNode);
+        Node prevNode = firstNode;
+        for (int i = 1; i < n; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            undirectedGraph.addNode(currentNode);
+            Edge currentEdge = graphModel.factory().newEdge(prevNode, currentNode, false);
+            undirectedGraph.addEdge(currentEdge);
+            prevNode = currentNode;
+        }
+        Edge currentEdge = graphModel.factory().newEdge(prevNode, firstNode, false);
+        undirectedGraph.addEdge(currentEdge);
+        return graphModel;
+    }
+
+    //generates graph from n+1 nodes
+    public static GraphModel generateStarUndirectedGraph(int n) {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node firstNode = graphModel.factory().newNode("0");
+        undirectedGraph.addNode(firstNode);
+        for (int i = 1; i <= n; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            undirectedGraph.addNode(currentNode);
+            Edge currentEdge = graphModel.factory().newEdge(firstNode, currentNode, false);
+            undirectedGraph.addEdge(currentEdge);
+        }
+        return graphModel;
+    }
+
+    public static GraphModel generateNullDirectedGraph(int n) {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        for (int i = 0; i < n; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            directedGraph.addNode(currentNode);
+        }
+        return graphModel;
+    }
+
+    public static GraphModel generateCompleteDirectedGraph(int n) {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node[] nodes = new Node[n];
+        for (int i = 0; i < n; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            nodes[i] = currentNode;
+            directedGraph.addNode(currentNode);
+        }
+        for (int i = 0; i < n - 1; i++) {
+            for (int j = i + 1; j < n; j++) {
+                Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j]);
+                directedGraph.addEdge(currentEdge);
+                currentEdge = graphModel.factory().newEdge(nodes[j], nodes[i]);
+                directedGraph.addEdge(currentEdge);
+            }
+        }
+        return graphModel;
+    }
+
+    public static GraphModel generatePathDirectedGraph(int n) {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        if (n <= 0) {
+            return graphModel;
+        }
+        Node firstNode = graphModel.factory().newNode("0");
+        directedGraph.addNode(firstNode);
+        Node prevNode = firstNode;
+        for (int i = 1; i < n; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            directedGraph.addNode(currentNode);
+            Edge currentEdge = graphModel.factory().newEdge(prevNode, currentNode);
+            directedGraph.addEdge(currentEdge);
+            prevNode = currentNode;
+        }
+        return graphModel;
+    }
+
+    public static GraphModel generateCyclicDirectedGraph(int n) {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        if (n <= 0) {
+            return graphModel;
+        }
+        Node firstNode = graphModel.factory().newNode("0");
+        directedGraph.addNode(firstNode);
+        Node prevNode = firstNode;
+        for (int i = 1; i < n; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            directedGraph.addNode(currentNode);
+            Edge currentEdge = graphModel.factory().newEdge(prevNode, currentNode);
+            directedGraph.addEdge(currentEdge);
+            prevNode = currentNode;
+        }
+        Edge currentEdge = graphModel.factory().newEdge(prevNode, firstNode);
+        directedGraph.addEdge(currentEdge);
+        return graphModel;
+    }
+}

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/HitsNGTest.java

@@ -0,0 +1,460 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import java.util.HashMap;
+import java.util.LinkedList;
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.graph.api.UndirectedGraph;
+import org.gephi.project.api.ProjectController;
+import org.gephi.project.impl.ProjectControllerImpl;
+import org.openide.util.Lookup;
+import static org.testng.Assert.*;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ *
+ * @author Anna
+ */
+public class HitsNGTest {
+
+    private ProjectController pc;
+
+    @BeforeClass
+    public void setUp() {
+        pc = Lookup.getDefault().lookup(ProjectControllerImpl.class);
+    }
+
+    @BeforeMethod
+    public void initialize() {
+        pc.newProject();
+    }
+
+    @AfterMethod
+    public void clean() {
+        pc.closeCurrentProject();
+    }
+
+    @Test
+    public void testOneNodeHits() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(1);
+        Graph hgraph = graphModel.getUndirectedGraph();
+
+        Hits hit = new Hits();
+
+        double[] authority = new double[1];
+        double[] hubs = new double[1];
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        hit.calculateHits(hgraph, hubs, authority, indicies, false, 0.01);
+
+        Node n1 = hgraph.getNode("0");
+        int index = indicies.get(n1);
+        double hub1 = hubs[index];
+        double auth1 = authority[index];
+
+        assertEquals(hub1, 1.0);
+        assertEquals(auth1, 1.0);
+    }
+
+    @Test
+    public void testTwoConnectedNodesHits() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(2);
+        Graph hgraph = graphModel.getUndirectedGraph();
+
+        Hits hit = new Hits();
+
+        double[] authority = new double[2];
+        double[] hubs = new double[2];
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        hit.calculateHits(hgraph, hubs, authority, indicies, false, 0.01);
+
+        Node n1 = hgraph.getNode("0");
+        Node n2 = hgraph.getNode("1");
+        int index1 = indicies.get(n1);
+        int index2 = indicies.get(n2);
+        double hub1 = hubs[index1];
+        double auth2 = authority[index2];
+
+        assertEquals(hub1, 0.5);
+        assertEquals(auth2, 0.5);
+    }
+
+    @Test
+    public void testNullGraphHits() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
+        Graph hgraph = graphModel.getUndirectedGraph();
+
+        Hits hit = new Hits();
+
+        double[] authority = new double[5];
+        double[] hubs = new double[5];
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        hit.calculateHits(hgraph, hubs, authority,indicies, false, 0.01);
+
+        Node n2 = hgraph.getNode("1");
+        Node n3 = hgraph.getNode("2");
+        int index2 = indicies.get(n2);
+        int index3 = indicies.get(n3);
+        double hub2 = hubs[index2];
+        double auth3 = authority[index3];
+
+        assertEquals(hub2, 0.2);
+        assertEquals(auth3, 0.2);
+    }
+
+    @Test
+    public void testCompleteGraphHits() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(5);
+        Graph hgraph = graphModel.getUndirectedGraph();
+
+        Hits hit = new Hits();
+
+        double[] authority = new double[5];
+        double[] hubs = new double[5];
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        hit.calculateHits(hgraph, hubs, authority, indicies, false, 0.01);
+
+        Node n1 = hgraph.getNode("0");
+        Node n5 = hgraph.getNode("4");
+        int index1 = indicies.get(n1);
+        int index5 = indicies.get(n5);
+        double hub1 = hubs[index1];
+        double auth5 = authority[index5];
+
+        assertEquals(hub1, 0.2);
+        assertEquals(auth5, 0.2);
+    }
+
+    @Test
+    public void testStarGraphHits() {
+        GraphModel graphModel = GraphGenerator.generateStarUndirectedGraph(5);
+        Graph hgraph = graphModel.getUndirectedGraph();
+
+        Hits hit = new Hits();
+
+        double[] authority = new double[6];
+        double[] hubs = new double[6];
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        hit.calculateHits(hgraph, hubs, authority, indicies, false, 0.01);
+
+        Node n1 = hgraph.getNode("0");
+        Node n3 = hgraph.getNode("2");
+        Node n4 = hgraph.getNode("3");
+        int index1 = indicies.get(n1);
+        int index3 = indicies.get(n3);
+        int index4 = indicies.get(n4);
+
+        double hub1 = hubs[index1];
+        double hub3 = hubs[index3];
+        double auth1 = authority[index1];
+        double auth4 = authority[index4];
+
+        boolean b1 = hub1 > hub3;
+        boolean b2 = auth1 > auth4;
+
+        assertTrue(b1);
+        assertTrue(b2);
+    }
+
+    @Test
+    public void testGraphWithSelfLoopsHits() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+
+        Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
+        Edge edge11 = graphModel.factory().newEdge(node1, node1, false);
+        Edge edge33 = graphModel.factory().newEdge(node3, node3, false);
+
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge11);
+        undirectedGraph.addEdge(edge33);
+
+        Graph hgraph = graphModel.getUndirectedGraph();
+
+        Hits hit = new Hits();
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        double[] authority = new double[3];
+        double[] hubs = new double[3];
+
+        hit.calculateHits(hgraph, hubs, authority, indicies, false, 0.01);
+
+        Node n1 = hgraph.getNode("0");
+        Node n2 = hgraph.getNode("1");
+        int index1 = indicies.get(n1);
+        int index2 = indicies.get(n2);
+
+        double hub1 = hubs[index1];
+        double hub2 = hubs[index2];
+
+        boolean b1 = hub2 > hub1;
+
+        assertTrue(b1);
+
+    }
+
+    @Test
+    public void testDirectedSpecial1GraphHits() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        directedGraph.addNode(node5);
+
+        Edge edge14 = graphModel.factory().newEdge(node1, node4);
+        Edge edge15 = graphModel.factory().newEdge(node1, node5);
+        Edge edge24 = graphModel.factory().newEdge(node2, node4);
+        Edge edge25 = graphModel.factory().newEdge(node2, node5);
+        Edge edge34 = graphModel.factory().newEdge(node3, node4);
+        Edge edge35 = graphModel.factory().newEdge(node3, node5);
+
+        directedGraph.addEdge(edge14);
+        directedGraph.addEdge(edge15);
+        directedGraph.addEdge(edge24);
+        directedGraph.addEdge(edge25);
+        directedGraph.addEdge(edge34);
+        directedGraph.addEdge(edge35);
+
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        Hits hit = new Hits();
+
+        double[] authority = new double[5];
+        double[] hubs = new double[5];
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        hit.calculateHits(hgraph, hubs, authority, indicies, true, 0.01);
+
+        Node n1 = hgraph.getNode("0");
+        Node n2 = hgraph.getNode("1");
+        Node n4 = hgraph.getNode("3");
+        Node n5 = hgraph.getNode("4");
+
+        int index1 = indicies.get(n1);
+        int index2 = indicies.get(n2);
+        int index4 = indicies.get(n4);
+        int index5 = indicies.get(n5);
+
+        double hub1 = hubs[index1];
+        double hub4 = hubs[index4];
+        double auth2 = authority[index2];
+        double auth5 = authority[index5];
+
+        double res = 0.333;
+        double diff = 0.01;
+
+        assertTrue(Math.abs(hub1 - res) < diff);
+        assertEquals(hub4, 0.);
+        assertEquals(auth2, 0.);
+        assertEquals(auth5, 0.5);
+    }
+
+    @Test
+    public void testDirectedStarOutGraphHits() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node firstNode = graphModel.factory().newNode("0");
+        directedGraph.addNode(firstNode);
+        for (int i = 1; i <= 5; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            directedGraph.addNode(currentNode);
+            Edge currentEdge = graphModel.factory().newEdge(firstNode, currentNode);
+            directedGraph.addEdge(currentEdge);
+        }
+
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+
+        Hits hit = new Hits();
+
+        double[] authority = new double[6];
+        double[] hubs = new double[6];
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        hit.calculateHits(hgraph, hubs, authority, indicies, true, 0.01);
+
+        Node n1 = hgraph.getNode("0");
+        Node n3 = hgraph.getNode("2");
+
+        int index1 = indicies.get(n1);
+        int index3 = indicies.get(n3);
+
+        double hub1 = hubs[index1];
+        double hub3 = hubs[index3];
+        double auth1 = authority[index1];
+        double auth3 = authority[index3];
+
+        double res = 0.146;
+        double diff = 0.01;
+
+        assertEquals(hub1, 1.);
+        assertEquals(auth1, 0.);
+        assertEquals(hub3, 0.);
+        assertEquals(auth3, 0.2);
+    }
+
+    @Test
+    public void testDirectedSpecial2GraphHits() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        Node node6 = graphModel.factory().newNode("5");
+
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        directedGraph.addNode(node5);
+        directedGraph.addNode(node6);
+
+        Edge edge21 = graphModel.factory().newEdge(node2, node1);
+        Edge edge31 = graphModel.factory().newEdge(node3, node1);
+        Edge edge41 = graphModel.factory().newEdge(node4, node1);
+        Edge edge51 = graphModel.factory().newEdge(node5, node1);
+        Edge edge36 = graphModel.factory().newEdge(node3, node6);
+        Edge edge46 = graphModel.factory().newEdge(node4, node6);
+        Edge edge56 = graphModel.factory().newEdge(node5, node6);
+
+        directedGraph.addEdge(edge21);
+        directedGraph.addEdge(edge31);
+        directedGraph.addEdge(edge41);
+        directedGraph.addEdge(edge51);
+        directedGraph.addEdge(edge36);
+        directedGraph.addEdge(edge46);
+        directedGraph.addEdge(edge56);
+
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        Hits hit = new Hits();
+
+        double[] authority = new double[6];
+        double[] hubs = new double[6];
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        hit.calculateHits(hgraph, hubs, authority, indicies, true, 0.01);
+
+        int index1 = indicies.get(node1);
+        int index2 = indicies.get(node2);
+        int index3 = indicies.get(node3);
+        int index5 = indicies.get(node5);
+        int index6 = indicies.get(node6);
+
+        double hub2 = hubs[index2];
+        double hub3 = hubs[index3];
+        double hub5 = hubs[index5];
+        double hub6 = hubs[index6];
+        double auth1 = authority[index1];
+        double auth3 = authority[index3];
+        double auth6 = authority[index6];
+
+        assertEquals(hub3, hub5);
+        assertTrue(hub3 > hub2);
+        assertTrue(auth1 > auth6);
+        assertEquals(hub6, 0.);
+        assertEquals(auth3, 0.);
+    }
+
+    @Test
+    public void testDirectedSpecial3GraphHits() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        Node node6 = graphModel.factory().newNode("5");
+
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        directedGraph.addNode(node5);
+        directedGraph.addNode(node6);
+
+        Edge edge15 = graphModel.factory().newEdge(node1, node5);
+        Edge edge25 = graphModel.factory().newEdge(node2, node5);
+        Edge edge35 = graphModel.factory().newEdge(node3, node5);
+        Edge edge45 = graphModel.factory().newEdge(node4, node5);
+        Edge edge56 = graphModel.factory().newEdge(node5, node6);
+
+        directedGraph.addEdge(edge15);
+        directedGraph.addEdge(edge25);
+        directedGraph.addEdge(edge35);
+        directedGraph.addEdge(edge45);
+        directedGraph.addEdge(edge56);
+
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        Hits hit = new Hits();
+
+        double[] authority = new double[6];
+        double[] hubs = new double[6];
+
+        HashMap<Node, Integer> indicies = hit.createIndiciesMap(hgraph);
+
+        hit.calculateHits(hgraph, hubs, authority, indicies, true, 0.01);
+
+        int index1 = indicies.get(node1);
+        int index3 = indicies.get(node3);
+        int index5 = indicies.get(node5);
+        int index6 = indicies.get(node6);
+
+        double hub1 = hubs[index1];
+        double hub3 = hubs[index3];
+        double hub5 = hubs[index5];
+        double auth5 = authority[index5];
+        double auth6 = authority[index6];
+
+        assertEquals(hub1, hub3);
+        assertTrue(hub1 > hub5);
+        assertTrue(auth5 > auth6);
+    }
+
+}

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/ModularityNGTest.java

@@ -0,0 +1,254 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import java.util.HashMap;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.graph.api.UndirectedGraph;
+import org.gephi.project.api.ProjectController;
+import org.gephi.project.impl.ProjectControllerImpl;
+import org.openide.util.Lookup;
+import static org.testng.Assert.*;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ *
+ * @author Anna
+ */
+public class ModularityNGTest {
+
+    private ProjectController pc;
+
+    @BeforeClass
+    public void setUp() {
+        pc = Lookup.getDefault().lookup(ProjectControllerImpl.class);
+    }
+
+    @BeforeMethod
+    public void initialize() {
+        pc.newProject();
+    }
+
+    @AfterMethod
+    public void clean() {
+        pc.closeCurrentProject();
+    }
+
+    @Test
+    public void testTwoConnectedNodesModularity() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(2);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        Modularity mod = new Modularity();
+
+        Modularity.CommunityStructure theStructure = mod.new CommunityStructure(hgraph);
+        int[] comStructure = new int[hgraph.getNodeCount()];
+
+        HashMap<String, Double> modularityValues = mod.computeModularity(hgraph, theStructure, comStructure,
+                1., true, false);
+
+        double modValue = modularityValues.get("modularity");
+        int class1 = comStructure[0];
+        int class2 = comStructure[1];
+
+        assertEquals(modValue, 0.0);
+        assertEquals(class1, class2);
+    }
+
+    @Test
+    public void testGraphWithouLinksModularity() {
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        Modularity mod = new Modularity();
+
+        Modularity.CommunityStructure theStructure = mod.new CommunityStructure(hgraph);
+        int[] comStructure = new int[hgraph.getNodeCount()];
+
+        HashMap<String, Double> modularityValues = mod.computeModularity(hgraph, theStructure, comStructure,
+                1., true, false);
+
+        double modValue = modularityValues.get("modularity");
+
+        assertEquals(modValue, Double.NaN);
+    }
+
+    @Test
+    public void testComputeBarbellGraphModularityNormalResolution() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node[] nodes = new Node[4];
+        for (int i = 0; i < 4; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
+            nodes[i] = currentNode;
+            undirectedGraph.addNode(currentNode);
+        }
+        for (int i = 0; i < 3; i++) {
+            for (int j = i + 1; j < 4; j++) {
+                Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
+                undirectedGraph.addEdge(currentEdge);
+            }
+        }
+        Edge currentEdge = graphModel.factory().newEdge(undirectedGraph.getNode("0"), undirectedGraph.getNode("5"), false);
+        undirectedGraph.addEdge(currentEdge);
+        UndirectedGraph graph = graphModel.getUndirectedGraph();
+
+        Modularity mod = new Modularity();
+
+        Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
+        int[] comStructure = new int[graph.getNodeCount()];
+
+        HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure,
+                1., true, false);
+
+        double modValue = modularityValues.get("modularity");
+
+        int class4 = comStructure[0];
+        int class5 = comStructure[5];
+
+        boolean correctResult = (class4 != class5 || modValue == 0.);
+
+        assertTrue(correctResult);
+    }
+
+    @Test
+    public void testComputeBarbellGraphHighResolution() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node[] nodes = new Node[4];
+        for (int i = 0; i < 4; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
+            nodes[i] = currentNode;
+            undirectedGraph.addNode(currentNode);
+        }
+        for (int i = 0; i < 3; i++) {
+            for (int j = i + 1; j < 4; j++) {
+                Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
+                undirectedGraph.addEdge(currentEdge);
+            }
+        }
+        Edge currentEdge = graphModel.factory().newEdge(undirectedGraph.getNode("0"), undirectedGraph.getNode("5"), false);
+        undirectedGraph.addEdge(currentEdge);
+        UndirectedGraph graph = graphModel.getUndirectedGraph();
+
+        Modularity mod = new Modularity();
+
+        Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
+        int[] comStructure = new int[graph.getNodeCount()];
+
+        HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure,
+                100., true, false);
+
+        double modValue = modularityValues.get("modularity");
+
+        int class4 = comStructure[0];
+        int class5 = comStructure[5];
+
+        assertEquals(modValue, 0.0);
+        assertEquals(class4, class5);
+    }
+
+    @Test
+    public void testComputeBarbellGraphModularityHasHighWeight() {
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node[] nodes = new Node[4];
+        for (int i = 0; i < 4; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
+            nodes[i] = currentNode;
+            undirectedGraph.addNode(currentNode);
+        }
+        for (int i = 0; i < 3; i++) {
+            for (int j = i + 1; j < 4; j++) {
+                Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
+                undirectedGraph.addEdge(currentEdge);
+            }
+        }
+        Edge currentEdge = graphModel.factory().newEdge(undirectedGraph.getNode("0"), undirectedGraph.getNode("5"), 0, 100.f, false);
+        undirectedGraph.addEdge(currentEdge);
+        UndirectedGraph graph = graphModel.getUndirectedGraph();
+
+        Modularity mod = new Modularity();
+
+        Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
+        int[] comStructure = new int[graph.getNodeCount()];
+
+        HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure,
+                1., true, true);
+
+        int class4 = comStructure[0];
+        int class5 = comStructure[5];
+
+        assertEquals(class4, class5);
+    }
+
+    @Test
+    public void testCyclicWithWeightsGraphModularity() {
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        Node node6 = graphModel.factory().newNode("5");
+        Node node7 = graphModel.factory().newNode("6");
+        Node node8 = graphModel.factory().newNode("7");
+
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+        undirectedGraph.addNode(node5);
+        undirectedGraph.addNode(node6);
+        undirectedGraph.addNode(node7);
+        undirectedGraph.addNode(node8);
+
+        Edge edge12 = graphModel.factory().newEdge(node1, node2, 0, 10.f, false);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
+        Edge edge34 = graphModel.factory().newEdge(node3, node4, 0, 10.f, false);
+        Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
+        Edge edge56 = graphModel.factory().newEdge(node5, node6, 0, 10.f, false);
+        Edge edge67 = graphModel.factory().newEdge(node6, node7, false);
+        Edge edge78 = graphModel.factory().newEdge(node7, node8, 0, 10.f, false);
+        Edge edge81 = graphModel.factory().newEdge(node8, node1, false);
+
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge34);
+        undirectedGraph.addEdge(edge45);
+        undirectedGraph.addEdge(edge56);
+        undirectedGraph.addEdge(edge67);
+        undirectedGraph.addEdge(edge78);
+        undirectedGraph.addEdge(edge81);
+
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+        Modularity mod = new Modularity();
+
+        Modularity.CommunityStructure theStructure = mod.new CommunityStructure(hgraph);
+        int[] comStructure = new int[hgraph.getNodeCount()];
+
+        HashMap<String, Double> modularityValues = mod.computeModularity(hgraph, theStructure, comStructure,
+                1., true, true);
+
+        int class1 = comStructure[0];
+        int class2 = comStructure[1];
+        int class4 = comStructure[3];
+        int class5 = comStructure[4];
+        int class7 = comStructure[6];
+        int class8 = comStructure[7];
+
+        assertEquals(class1, class2);
+        assertEquals(class7, class8);
+        assertNotEquals(class4, class5);
+    }
+}

modules/StatisticsPlugin/src/test/java/org/gephi/statistics/plugin/PageRankNGTest.java

@@ -0,0 +1,450 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.statistics.plugin;
+
+import java.util.HashMap;
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.UndirectedGraph;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.GraphController;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.project.api.ProjectController;
+import org.gephi.project.impl.ProjectControllerImpl;
+import org.openide.util.Lookup;
+import static org.testng.Assert.*;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ *
+ * @author Anna
+ */
+public class PageRankNGTest {
+
+    private ProjectController pc;
+
+    @BeforeClass
+    public void setUp() {
+        pc = Lookup.getDefault().lookup(ProjectControllerImpl.class);
+    }
+
+    @BeforeMethod
+    public void initialize() {
+        pc.newProject();
+    }
+
+    @AfterMethod
+    public void clean() {
+        pc.closeCurrentProject();
+    }
+
+    @Test
+    public void testOneNodePageRank() {
+        pc.newProject();
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(1);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, false, false, 0.001, 0.85);
+
+        Node n1 = hgraph.getNode("0");
+        int index = indicies.get(n1);
+        double pr1 = pageRank[index];
+
+        assertEquals(pr1, 1.0);
+    }
+
+    @Test
+    public void testTwoConnectedNodesPageRank() {
+        pc.newProject();
+        GraphModel graphModel = GraphGenerator.generatePathUndirectedGraph(2);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, false, false, 0.001, 0.85);
+
+        Node n2 = hgraph.getNode("1");
+        int index = indicies.get(n2);
+        double pr2 = pageRank[index];
+
+        assertEquals(pr2, 0.5);
+    }
+
+    @Test
+    public void testNullGraphPageRank() {
+        pc.newProject();
+        GraphModel graphModel = GraphGenerator.generateNullUndirectedGraph(5);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, false, false, 0.001, 0.85);
+
+        Node n1 = hgraph.getNode("0");
+        Node n4 = hgraph.getNode("3");
+        int index1 = indicies.get(n1);
+        int index4 = indicies.get(n4);
+        double pr1 = pageRank[index1];
+        double pr4 = pageRank[index4];
+        double res = 0.2d;
+
+        double diff1 = Math.abs(pr1 - res);
+        double diff4 = Math.abs(pr4 - res);
+        assertTrue(diff1 < 0.01);
+        assertTrue(diff4 < 0.01);
+        assertEquals(pr1, pr4);
+    }
+
+    @Test
+    public void testCompleteGraphPageRank() {
+        pc.newProject();
+        GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(5);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, false, false, 0.001, 0.85);
+
+        Node n2 = hgraph.getNode("2");
+        int index2 = indicies.get(n2);
+        double pr2 = pageRank[index2];
+        double res = 0.2d;
+
+        double diff2 = Math.abs(pr2 - res);
+        assertTrue(diff2 < 0.01);
+    }
+
+    @Test
+    public void testCyclicGraphPageRank() {
+        pc.newProject();
+        GraphModel graphModel = GraphGenerator.generateCyclicUndirectedGraph(6);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, false, false, 0.001, 0.6);
+
+        Node n4 = hgraph.getNode("3");
+        int index4 = indicies.get(n4);
+        double pr4 = pageRank[index4];
+        double res = 0.1667;
+
+        double diff4 = Math.abs(pr4 - res);
+        assertTrue(diff4 < 0.01);
+    }
+
+    @Test
+    public void testStarGraphPageRank() {
+        pc.newProject();
+        GraphModel graphModel = GraphGenerator.generateStarUndirectedGraph(5);
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, false, false, 0.001, 0.6);
+
+        Node n1 = hgraph.getNode("0");
+        Node n2 = hgraph.getNode("1");
+        Node n3 = hgraph.getNode("2");
+        Node n4 = hgraph.getNode("3");
+        Node n5 = hgraph.getNode("4");
+        Node n6 = hgraph.getNode("5");
+
+        int index1 = indicies.get(n1);
+        int index2 = indicies.get(n2);
+        int index3 = indicies.get(n3);
+        int index4 = indicies.get(n4);
+        int index5 = indicies.get(n5);
+        int index6 = indicies.get(n6);
+
+        double pr1 = pageRank[index1];
+        double pr2 = pageRank[index2];
+        double pr3 = pageRank[index3];
+        double pr4 = pageRank[index4];
+        double pr5 = pageRank[index5];
+        double pr6 = pageRank[index6];
+
+        boolean oneMoreThree = pr1 > pr3;
+        double res = 1.;
+        double diff = 0.01;
+        double sum = pr1 + pr2 + pr3 + pr4 + pr5 + pr6;
+
+        assertTrue(oneMoreThree);
+        assertEquals(pr2, pr4);
+        assertTrue(Math.abs(sum - res) < diff);
+    }
+
+    @Test
+    public void testPathDirectedGraphPageRank() {
+        pc.newProject();
+        GraphModel graphModel = GraphGenerator.generatePathDirectedGraph(4);
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, true, false, 0.001, 0.85);
+
+        Node n1 = hgraph.getNode("0");
+        Node n2 = hgraph.getNode("1");
+        Node n3 = hgraph.getNode("2");
+        Node n4 = hgraph.getNode("3");
+
+        int index1 = indicies.get(n1);
+        int index2 = indicies.get(n2);
+        int index3 = indicies.get(n3);
+        int index4 = indicies.get(n4);
+
+        double pr1 = pageRank[index1];
+        double pr2 = pageRank[index2];
+        double pr3 = pageRank[index3];
+        double pr4 = pageRank[index4];
+
+        double res = 1.;
+        double diff = 0.01;
+        double sum = pr1 + pr2 + pr3 + pr4;
+
+        assertTrue(pr1 < pr2);
+        assertTrue(pr2 < pr4);
+        assertTrue(Math.abs(sum - res) < diff);
+    }
+
+    @Test
+    public void testCyclicDirectedGraphPageRank() {
+        pc.newProject();
+        GraphModel graphModel = GraphGenerator.generateCyclicDirectedGraph(5);
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, true, false, 0.001, 0.85);
+
+        Node n3 = hgraph.getNode("2");
+
+        int index3 = indicies.get(n3);
+
+        double pr3 = pageRank[index3];
+        double res = 0.2d;
+
+        double diff3 = Math.abs(pr3 - res);
+        assertTrue(diff3 < 0.01);
+    }
+
+    @Test
+    public void testDirectedSpecial1GraphPageRank() {
+        pc.newProject();
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        Node node6 = graphModel.factory().newNode("5");
+        Node node7 = graphModel.factory().newNode("6");
+        Node node8 = graphModel.factory().newNode("7");
+        Node node9 = graphModel.factory().newNode("8");
+
+        directedGraph.addNode(node1);
+        directedGraph.addNode(node2);
+        directedGraph.addNode(node3);
+        directedGraph.addNode(node4);
+        directedGraph.addNode(node5);
+        directedGraph.addNode(node6);
+        directedGraph.addNode(node7);
+        directedGraph.addNode(node8);
+        directedGraph.addNode(node9);
+
+        Edge edge12 = graphModel.factory().newEdge(node1, node2);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3);
+        Edge edge31 = graphModel.factory().newEdge(node3, node1);
+        Edge edge14 = graphModel.factory().newEdge(node1, node4);
+        Edge edge45 = graphModel.factory().newEdge(node4, node5);
+        Edge edge51 = graphModel.factory().newEdge(node5, node1);
+        Edge edge16 = graphModel.factory().newEdge(node1, node6);
+        Edge edge67 = graphModel.factory().newEdge(node6, node7);
+        Edge edge71 = graphModel.factory().newEdge(node7, node1);
+        Edge edge18 = graphModel.factory().newEdge(node1, node8);
+        Edge edge89 = graphModel.factory().newEdge(node8, node9);
+        Edge edge91 = graphModel.factory().newEdge(node9, node1);
+
+        directedGraph.addEdge(edge12);
+        directedGraph.addEdge(edge23);
+        directedGraph.addEdge(edge31);
+        directedGraph.addEdge(edge14);
+        directedGraph.addEdge(edge45);
+        directedGraph.addEdge(edge51);
+        directedGraph.addEdge(edge16);
+        directedGraph.addEdge(edge67);
+        directedGraph.addEdge(edge71);
+        directedGraph.addEdge(edge18);
+        directedGraph.addEdge(edge89);
+        directedGraph.addEdge(edge91);
+
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, true, false, 0.001, 0.85);
+
+        int index1 = indicies.get(node1);
+        int index2 = indicies.get(node2);
+        int index3 = indicies.get(node3);
+
+        double pr1 = pageRank[index1];
+        double pr2 = pageRank[index2];
+        double pr3 = pageRank[index3];
+
+        assertTrue(pr1 > pr2);
+        assertTrue(pr2 < pr3);
+    }
+
+    @Test
+    public void testDirectedStarOutGraphPageRank() {
+        pc.newProject();
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        DirectedGraph directedGraph = graphModel.getDirectedGraph();
+        Node firstNode = graphModel.factory().newNode("0");
+        directedGraph.addNode(firstNode);
+        for (int i = 1; i <= 5; i++) {
+            Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
+            directedGraph.addNode(currentNode);
+            Edge currentEdge = graphModel.factory().newEdge(firstNode, currentNode);
+            directedGraph.addEdge(currentEdge);
+        }
+
+        DirectedGraph hgraph = graphModel.getDirectedGraph();
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, true, false, 0.001, 0.85);
+
+        Node n1 = hgraph.getNode("0");
+        Node n2 = hgraph.getNode("1");
+        Node n3 = hgraph.getNode("2");
+        Node n5 = hgraph.getNode("4");
+
+        int index1 = indicies.get(n1);
+        int index2 = indicies.get(n2);
+        int index3 = indicies.get(n3);
+        int index5 = indicies.get(n5);
+
+        double pr1 = pageRank[index1];
+        double pr2 = pageRank[index2];
+        double pr3 = pageRank[index3];
+        double pr5 = pageRank[index5];
+
+        double res = 0.146;
+        double diff = 0.01;
+
+        assertTrue(pr1 < pr3);
+        assertEquals(pr2, pr5);
+        assertTrue(Math.abs(pr1 - res) < diff);
+    }
+
+    @Test
+    public void testUndirectedWeightedGraphPageRank() {
+        pc.newProject();
+        GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
+
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
+        Node node1 = graphModel.factory().newNode("0");
+        Node node2 = graphModel.factory().newNode("1");
+        Node node3 = graphModel.factory().newNode("2");
+        Node node4 = graphModel.factory().newNode("3");
+        Node node5 = graphModel.factory().newNode("4");
+        Node node6 = graphModel.factory().newNode("5");
+
+        undirectedGraph.addNode(node1);
+        undirectedGraph.addNode(node2);
+        undirectedGraph.addNode(node3);
+        undirectedGraph.addNode(node4);
+        undirectedGraph.addNode(node5);
+        undirectedGraph.addNode(node6);
+
+        Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
+        Edge edge23 = graphModel.factory().newEdge(node2, node3, 0, 10, false);
+        Edge edge34 = graphModel.factory().newEdge(node3, node4, false);
+        Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
+        Edge edge56 = graphModel.factory().newEdge(node5, node6, false);
+        Edge edge61 = graphModel.factory().newEdge(node6, node1, false);
+
+        undirectedGraph.addEdge(edge12);
+        undirectedGraph.addEdge(edge23);
+        undirectedGraph.addEdge(edge34);
+        undirectedGraph.addEdge(edge45);
+        undirectedGraph.addEdge(edge56);
+        undirectedGraph.addEdge(edge61);
+
+        UndirectedGraph hgraph = graphModel.getUndirectedGraph();
+        PageRank pr = new PageRank();
+
+        double[] pageRank;
+
+        HashMap<Node, Integer> indicies = pr.createIndiciesMap(hgraph);
+
+        pageRank = pr.calculatePagerank(hgraph, indicies, false, true, 0.001, 0.85);
+
+        int index1 = indicies.get(node1);
+        int index2 = indicies.get(node2);
+        int index3 = indicies.get(node3);
+        int index6 = indicies.get(node6);
+
+        double diff = 0.01;
+
+        double pr1 = pageRank[index1];
+        double pr2 = pageRank[index2];
+        double pr3 = pageRank[index3];
+        double pr6 = pageRank[index6];
+
+        assertTrue(Math.abs(pr2 - pr3) < diff);
+        assertTrue(pr1 < pr2);
+        assertTrue(pr1 < pr6);
+    }
+}

modules/StatisticsPluginUI/pom.xml

@@ -16,10 +16,6 @@
     <name>StatisticsPluginUI</name>
 
     <dependencies>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>data-attributes-api</artifactId>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>dynamic-api</artifactId>

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/ClusteringCoefficientPanel.form

@@ -1,4 +1,4 @@
-<?xml version="1.1" encoding="UTF-8" ?>
+<?xml version="1.0" encoding="UTF-8" ?>
 
 <Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
   <NonVisualComponents>
@@ -29,7 +29,7 @@
                   <Component id="undirectedRadioButton" alignment="0" min="-2" max="-2" attributes="0"/>
                   <Component id="directedRadioButton" alignment="0" min="-2" max="-2" attributes="0"/>
               </Group>
-              <EmptySpace pref="519" max="32767" attributes="0"/>
+              <EmptySpace pref="532" max="32767" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/ClusteringCoefficientPanel.java

@@ -55,7 +55,7 @@ public class ClusteringCoefficientPanel extends javax.swing.JPanel {
         
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if(graphController.getModel().isUndirected()){
+        if(graphController.getGraphModel().isUndirected()){
             directedRadioButton.setEnabled(false);
         }
     }
@@ -113,7 +113,7 @@ public class ClusteringCoefficientPanel extends javax.swing.JPanel {
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                     .addComponent(undirectedRadioButton)
                     .addComponent(directedRadioButton))
-                .addContainerGap(519, Short.MAX_VALUE))
+                .addContainerGap(532, Short.MAX_VALUE))
         );
         layout.setVerticalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/ConnectedComponentPanel.form

@@ -1,4 +1,4 @@
-<?xml version="1.1" encoding="UTF-8" ?>
+<?xml version="1.0" encoding="UTF-8" ?>
 
 <Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
   <NonVisualComponents>
@@ -27,7 +27,7 @@
                   <Component id="directedRadioButton" alignment="0" min="-2" max="-2" attributes="0"/>
                   <Component id="undirectedRadioButton" alignment="0" min="-2" max="-2" attributes="0"/>
               </Group>
-              <EmptySpace pref="26" max="32767" attributes="0"/>
+              <EmptySpace pref="39" max="32767" attributes="0"/>
               <Group type="103" groupAlignment="0" max="-2" attributes="0">
                   <Component id="jLabel2" max="32767" attributes="1"/>
                   <Component id="jLabel1" alignment="0" pref="420" max="32767" attributes="1"/>

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/ConnectedComponentPanel.java

@@ -56,7 +56,7 @@ public class ConnectedComponentPanel extends javax.swing.JPanel {
         
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if(graphController.getModel().isUndirected()){
+        if(graphController.getGraphModel().isUndirected()){
             directedRadioButton.setEnabled(false);
         }
     }
@@ -115,7 +115,7 @@ public class ConnectedComponentPanel extends javax.swing.JPanel {
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                     .addComponent(directedRadioButton)
                     .addComponent(undirectedRadioButton))
-                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 26, Short.MAX_VALUE)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 39, Short.MAX_VALUE)
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
                     .addComponent(jLabel2, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                     .addComponent(jLabel1, javax.swing.GroupLayout.DEFAULT_SIZE, 420, Short.MAX_VALUE)))

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/DegreeDistributionPanel.form

@@ -1,4 +1,4 @@
-<?xml version="1.1" encoding="UTF-8" ?>
+<?xml version="1.0" encoding="UTF-8" ?>
 
 <Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
   <NonVisualComponents>
@@ -76,11 +76,11 @@
     </Component>
     <Component class="org.jdesktop.swingx.JXLabel" name="descriptionLabel">
       <Properties>
-        <Property name="lineWrap" type="boolean" value="true"/>
         <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
           <ResourceString bundle="org/gephi/ui/statistics/plugin/Bundle.properties" key="DegreeDistributionPanel.descriptionLabel.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
         </Property>
         <Property name="verticalAlignment" type="int" value="1"/>
+        <Property name="lineWrap" type="boolean" value="true"/>
       </Properties>
     </Component>
     <Component class="org.jdesktop.swingx.JXHeader" name="header">

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/DegreeDistributionPanel.java

@@ -55,7 +55,7 @@ public class DegreeDistributionPanel extends javax.swing.JPanel {
         
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if(graphController.getModel().isUndirected()){
+        if(graphController.getGraphModel().isUndirected()){
             directedRadioButton.setEnabled(false);
         }
     }
@@ -103,7 +103,7 @@ public class DegreeDistributionPanel extends javax.swing.JPanel {
         this.setLayout(layout);
         layout.setHorizontalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addComponent(header, javax.swing.GroupLayout.DEFAULT_SIZE, 419, Short.MAX_VALUE)
+            .addComponent(header, javax.swing.GroupLayout.DEFAULT_SIZE, 439, Short.MAX_VALUE)
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
@@ -121,7 +121,7 @@ public class DegreeDistributionPanel extends javax.swing.JPanel {
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                 .addComponent(undirectedRadioButton)
                 .addGap(96, 96, 96)
-                .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, 2, Short.MAX_VALUE)
+                .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                 .addContainerGap())
         );
     }// </editor-fold>//GEN-END:initComponents

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/EigenvectorCentralityPanel.form

@@ -1,4 +1,4 @@
-<?xml version="1.1" encoding="UTF-8" ?>
+<?xml version="1.0" encoding="UTF-8" ?>
 
 <Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
   <NonVisualComponents>
@@ -21,22 +21,18 @@
     <DimensionLayout dim="0">
       <Group type="103" groupAlignment="0" attributes="0">
           <Component id="header" alignment="0" pref="541" max="32767" attributes="0"/>
-          <Group type="102" alignment="0" attributes="0">
+          <Group type="102" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
-              <Component id="directedRadioButton" min="-2" max="-2" attributes="0"/>
-              <EmptySpace pref="439" max="32767" attributes="0"/>
-          </Group>
-          <Group type="102" alignment="0" attributes="0">
-              <EmptySpace max="-2" attributes="0"/>
-              <Component id="undirectedRadioButton" min="-2" max="-2" attributes="0"/>
-              <EmptySpace pref="422" max="32767" attributes="0"/>
-          </Group>
-          <Group type="102" alignment="0" attributes="0">
-              <EmptySpace max="-2" attributes="0"/>
-              <Component id="jLabel1" min="-2" max="-2" attributes="0"/>
-              <EmptySpace min="-2" pref="8" max="-2" attributes="0"/>
-              <Component id="iterationTextField" min="-2" pref="174" max="-2" attributes="0"/>
-              <EmptySpace pref="204" max="32767" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Component id="directedRadioButton" alignment="0" min="-2" max="-2" attributes="0"/>
+                  <Component id="undirectedRadioButton" alignment="0" min="-2" max="-2" attributes="0"/>
+                  <Group type="102" alignment="0" attributes="0">
+                      <Component id="jLabel1" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="-2" pref="8" max="-2" attributes="0"/>
+                      <Component id="iterationTextField" min="-2" pref="174" max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+              <EmptySpace max="32767" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/EigenvectorCentralityPanel.java

@@ -56,7 +56,7 @@ public class EigenvectorCentralityPanel extends javax.swing.JPanel {
         
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if(graphController.getModel().isUndirected()){
+        if(graphController.getGraphModel().isUndirected()){
             directedRadioButton.setEnabled(false);
         }
     }
@@ -127,18 +127,14 @@ public class EigenvectorCentralityPanel extends javax.swing.JPanel {
             .addComponent(header, javax.swing.GroupLayout.DEFAULT_SIZE, 541, Short.MAX_VALUE)
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
-                .addComponent(directedRadioButton)
-                .addContainerGap(439, Short.MAX_VALUE))
-            .addGroup(layout.createSequentialGroup()
-                .addContainerGap()
-                .addComponent(undirectedRadioButton)
-                .addContainerGap(422, Short.MAX_VALUE))
-            .addGroup(layout.createSequentialGroup()
-                .addContainerGap()
-                .addComponent(jLabel1)
-                .addGap(8, 8, 8)
-                .addComponent(iterationTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 174, javax.swing.GroupLayout.PREFERRED_SIZE)
-                .addContainerGap(204, Short.MAX_VALUE))
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(directedRadioButton)
+                    .addComponent(undirectedRadioButton)
+                    .addGroup(layout.createSequentialGroup()
+                        .addComponent(jLabel1)
+                        .addGap(8, 8, 8)
+                        .addComponent(iterationTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 174, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
         layout.setVerticalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/GraphDensityPanel.form

@@ -1,4 +1,4 @@
-<?xml version="1.1" encoding="UTF-8" ?>
+<?xml version="1.0" encoding="UTF-8" ?>
 
 <Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
   <NonVisualComponents>
@@ -21,15 +21,13 @@
     <DimensionLayout dim="0">
       <Group type="103" groupAlignment="0" attributes="0">
           <Component id="header" alignment="0" pref="477" max="32767" attributes="0"/>
-          <Group type="102" alignment="0" attributes="0">
+          <Group type="102" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
-              <Component id="undirectedRadioButton" min="-2" max="-2" attributes="0"/>
-              <EmptySpace pref="358" max="32767" attributes="0"/>
-          </Group>
-          <Group type="102" alignment="0" attributes="0">
-              <EmptySpace max="-2" attributes="0"/>
-              <Component id="directedRadioButton" min="-2" max="-2" attributes="0"/>
-              <EmptySpace pref="375" max="32767" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Component id="undirectedRadioButton" alignment="0" min="-2" max="-2" attributes="0"/>
+                  <Component id="directedRadioButton" alignment="0" min="-2" max="-2" attributes="0"/>
+              </Group>
+              <EmptySpace max="32767" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/GraphDensityPanel.java

@@ -55,7 +55,7 @@ public class GraphDensityPanel extends javax.swing.JPanel {
         
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if(graphController.getModel().isUndirected()){
+        if(graphController.getGraphModel().isUndirected()){
             directedRadioButton.setEnabled(false);
         }
     }
@@ -98,15 +98,13 @@ public class GraphDensityPanel extends javax.swing.JPanel {
         this.setLayout(layout);
         layout.setHorizontalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addComponent(header, javax.swing.GroupLayout.DEFAULT_SIZE, 443, Short.MAX_VALUE)
+            .addComponent(header, javax.swing.GroupLayout.DEFAULT_SIZE, 477, Short.MAX_VALUE)
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
-                .addComponent(undirectedRadioButton)
-                .addContainerGap(358, Short.MAX_VALUE))
-            .addGroup(layout.createSequentialGroup()
-                .addContainerGap()
-                .addComponent(directedRadioButton)
-                .addContainerGap(372, Short.MAX_VALUE))
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(undirectedRadioButton)
+                    .addComponent(directedRadioButton))
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
         layout.setVerticalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/GraphDistancePanel.form

@@ -1,4 +1,4 @@
-<?xml version="1.1" encoding="UTF-8" ?>
+<?xml version="1.0" encoding="UTF-8" ?>
 
 <Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
   <NonVisualComponents>
@@ -20,40 +20,43 @@
   <Layout>
     <DimensionLayout dim="0">
       <Group type="103" groupAlignment="0" attributes="0">
-          <Component id="header" alignment="0" pref="747" max="32767" attributes="0"/>
+          <Component id="header" alignment="0" pref="0" max="32767" attributes="0"/>
           <Group type="102" alignment="0" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
               <Group type="103" groupAlignment="0" attributes="0">
                   <Group type="102" alignment="0" attributes="0">
                       <EmptySpace min="-2" pref="262" max="-2" attributes="0"/>
-                      <Component id="descriptionLabel" pref="448" max="32767" attributes="0"/>
+                      <Component id="descriptionLabel" max="32767" attributes="0"/>
                       <EmptySpace max="-2" attributes="0"/>
                   </Group>
                   <Group type="102" alignment="0" attributes="0">
                       <Component id="directedRadioButton" min="-2" max="-2" attributes="0"/>
-                      <EmptySpace pref="260" max="32767" attributes="0"/>
+                      <EmptySpace max="32767" attributes="0"/>
                       <Component id="normalizeButton" min="-2" max="-2" attributes="0"/>
                       <EmptySpace min="-2" pref="165" max="-2" attributes="0"/>
                   </Group>
               </Group>
           </Group>
-          <Group type="102" alignment="0" attributes="0">
-              <EmptySpace max="-2" attributes="0"/>
-              <Component id="undirectedRadioButton" min="-2" max="-2" attributes="0"/>
-              <EmptySpace pref="628" max="32767" attributes="0"/>
-          </Group>
-          <Group type="102" alignment="0" attributes="0">
+          <Group type="102" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
               <Group type="103" groupAlignment="0" attributes="0">
-                  <Component id="jLabel2" alignment="0" min="-2" max="-2" attributes="1"/>
-                  <Component id="jLabel1" alignment="0" min="-2" max="-2" attributes="1"/>
-                  <Component id="jLabel3" min="-2" max="-2" attributes="0"/>
-              </Group>
-              <EmptySpace max="-2" attributes="0"/>
-              <Group type="103" groupAlignment="0" attributes="0">
-                  <Component id="jXLabel3" max="32767" attributes="0"/>
-                  <Component id="jXLabel2" max="32767" attributes="0"/>
-                  <Component id="jXLabel1" alignment="1" max="32767" attributes="0"/>
+                  <Group type="102" alignment="0" attributes="0">
+                      <Component id="undirectedRadioButton" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                  </Group>
+                  <Group type="102" alignment="0" attributes="0">
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="jLabel2" alignment="0" min="-2" max="-2" attributes="1"/>
+                          <Component id="jLabel1" alignment="0" min="-2" max="-2" attributes="1"/>
+                          <Component id="jLabel3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="jXLabel3" max="32767" attributes="0"/>
+                          <Component id="jXLabel2" max="32767" attributes="0"/>
+                          <Component id="jXLabel1" alignment="1" max="32767" attributes="0"/>
+                      </Group>
+                  </Group>
               </Group>
               <EmptySpace max="-2" attributes="0"/>
           </Group>
@@ -124,11 +127,11 @@
     </Component>
     <Component class="org.jdesktop.swingx.JXLabel" name="descriptionLabel">
       <Properties>
-        <Property name="lineWrap" type="boolean" value="true"/>
         <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
           <ResourceString bundle="org/gephi/ui/statistics/plugin/Bundle.properties" key="GraphDistancePanel.descriptionLabel.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
         </Property>
         <Property name="verticalAlignment" type="int" value="1"/>
+        <Property name="lineWrap" type="boolean" value="true"/>
       </Properties>
     </Component>
     <Component class="org.jdesktop.swingx.JXHeader" name="header">
@@ -143,26 +146,26 @@
     </Component>
     <Component class="org.jdesktop.swingx.JXLabel" name="jXLabel1">
       <Properties>
-        <Property name="lineWrap" type="boolean" value="true"/>
         <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
           <ResourceString bundle="org/gephi/ui/statistics/plugin/Bundle.properties" key="GraphDistancePanel.jXLabel1.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
         </Property>
+        <Property name="lineWrap" type="boolean" value="true"/>
       </Properties>
     </Component>
     <Component class="org.jdesktop.swingx.JXLabel" name="jXLabel2">
       <Properties>
-        <Property name="lineWrap" type="boolean" value="true"/>
         <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
           <ResourceString bundle="org/gephi/ui/statistics/plugin/Bundle.properties" key="GraphDistancePanel.jXLabel2.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
         </Property>
+        <Property name="lineWrap" type="boolean" value="true"/>
       </Properties>
     </Component>
     <Component class="org.jdesktop.swingx.JXLabel" name="jXLabel3">
       <Properties>
-        <Property name="lineWrap" type="boolean" value="true"/>
         <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
           <ResourceString bundle="org/gephi/ui/statistics/plugin/Bundle.properties" key="GraphDistancePanel.jXLabel3.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
         </Property>
+        <Property name="lineWrap" type="boolean" value="true"/>
       </Properties>
     </Component>
     <Component class="javax.swing.JLabel" name="jLabel1">

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/GraphDistancePanel.java

@@ -55,7 +55,7 @@ public class GraphDistancePanel extends javax.swing.JPanel {
         
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if(graphController.getModel().isUndirected()){
+        if(graphController.getGraphModel().isUndirected()){
             directedRadioButton.setEnabled(false);
         }
     }
@@ -146,34 +146,35 @@ public class GraphDistancePanel extends javax.swing.JPanel {
         this.setLayout(layout);
         layout.setHorizontalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addComponent(header, javax.swing.GroupLayout.DEFAULT_SIZE, 747, Short.MAX_VALUE)
+            .addComponent(header, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                     .addGroup(layout.createSequentialGroup()
                         .addGap(262, 262, 262)
-                        .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, 448, Short.MAX_VALUE)
+                        .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                         .addContainerGap())
                     .addGroup(layout.createSequentialGroup()
                         .addComponent(directedRadioButton)
-                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 260, Short.MAX_VALUE)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                         .addComponent(normalizeButton)
                         .addGap(165, 165, 165))))
-            .addGroup(layout.createSequentialGroup()
-                .addContainerGap()
-                .addComponent(undirectedRadioButton)
-                .addContainerGap(628, Short.MAX_VALUE))
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addComponent(jLabel2)
-                    .addComponent(jLabel1)
-                    .addComponent(jLabel3))
-                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addComponent(jXLabel3, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
-                    .addComponent(jXLabel2, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
-                    .addComponent(jXLabel1, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                    .addGroup(layout.createSequentialGroup()
+                        .addComponent(undirectedRadioButton)
+                        .addGap(0, 0, Short.MAX_VALUE))
+                    .addGroup(layout.createSequentialGroup()
+                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                            .addComponent(jLabel2)
+                            .addComponent(jLabel1)
+                            .addComponent(jLabel3))
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                            .addComponent(jXLabel3, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                            .addComponent(jXLabel2, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                            .addComponent(jXLabel1, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))))
                 .addContainerGap())
         );
         layout.setVerticalGroup(
@@ -199,7 +200,7 @@ public class GraphDistancePanel extends javax.swing.JPanel {
                     .addComponent(jLabel3, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                     .addComponent(jXLabel3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                 .addGap(20, 20, 20)
-                .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, 10, Short.MAX_VALUE)
+                .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                 .addContainerGap())
         );
     }// </editor-fold>//GEN-END:initComponents

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/HitsPanel.form

@@ -1,4 +1,4 @@
-<?xml version="1.1" encoding="UTF-8" ?>
+<?xml version="1.0" encoding="UTF-8" ?>
 
 <Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
   <NonVisualComponents>
@@ -120,11 +120,11 @@
     </Component>
     <Component class="org.jdesktop.swingx.JXLabel" name="descriptionLabel">
       <Properties>
-        <Property name="lineWrap" type="boolean" value="true"/>
         <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
           <ResourceString bundle="org/gephi/ui/statistics/plugin/Bundle.properties" key="HitsPanel.descriptionLabel.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
         </Property>
         <Property name="verticalAlignment" type="int" value="1"/>
+        <Property name="lineWrap" type="boolean" value="true"/>
       </Properties>
     </Component>
     <Component class="org.jdesktop.swingx.JXHeader" name="header">
@@ -142,7 +142,6 @@
         <Property name="foreground" type="java.awt.Color" editor="org.netbeans.beaninfo.editors.ColorEditor">
           <Color blue="66" green="66" red="66" type="rgb"/>
         </Property>
-        <Property name="lineWrap" type="boolean" value="true"/>
         <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
           <ResourceString bundle="org/gephi/ui/statistics/plugin/Bundle.properties" key="HitsPanel.epsilonLabel.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
         </Property>
@@ -151,6 +150,7 @@
             <Font component="epsilonLabel" property="font" relativeSize="true" size="-1"/>
           </FontInfo>
         </Property>
+        <Property name="lineWrap" type="boolean" value="true"/>
       </Properties>
     </Component>
   </SubComponents>

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/HitsPanel.java

@@ -55,7 +55,7 @@ public class HitsPanel extends javax.swing.JPanel {
         
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if(graphController.getModel().isUndirected()){
+        if(graphController.getGraphModel().isUndirected()){
             directedRadioButton.setEnabled(false);
         }
     }
@@ -129,11 +129,11 @@ public class HitsPanel extends javax.swing.JPanel {
         this.setLayout(layout);
         layout.setHorizontalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addComponent(header, javax.swing.GroupLayout.DEFAULT_SIZE, 440, Short.MAX_VALUE)
+            .addComponent(header, javax.swing.GroupLayout.DEFAULT_SIZE, 662, Short.MAX_VALUE)
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, 420, Short.MAX_VALUE)
+                    .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, 622, Short.MAX_VALUE)
                     .addGroup(layout.createSequentialGroup()
                         .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                             .addComponent(directedRadioButton)
@@ -162,7 +162,7 @@ public class HitsPanel extends javax.swing.JPanel {
                     .addComponent(undirectedRadioButton)
                     .addComponent(epsilonLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                 .addGap(59, 59, 59)
-                .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, 39, Short.MAX_VALUE)
+                .addComponent(descriptionLabel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                 .addContainerGap())
         );
     }// </editor-fold>//GEN-END:initComponents

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/PageRankPanel.form

@@ -1,4 +1,4 @@
-<?xml version="1.1" encoding="UTF-8" ?>
+<?xml version="1.0" encoding="UTF-8" ?>
 
 <Form version="1.5" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
   <NonVisualComponents>
@@ -20,7 +20,7 @@
   <Layout>
     <DimensionLayout dim="0">
       <Group type="103" groupAlignment="0" attributes="0">
-          <Component id="jXHeader1" alignment="0" pref="605" max="32767" attributes="0"/>
+          <Component id="jXHeader1" alignment="0" pref="0" max="32767" attributes="0"/>
           <Group type="102" alignment="0" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
               <Group type="103" groupAlignment="0" attributes="0">

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/PageRankPanel.java

@@ -55,7 +55,7 @@ public class PageRankPanel extends javax.swing.JPanel {
         
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if(graphController.getModel().isUndirected()){
+        if(graphController.getGraphModel().isUndirected()){
             directedRadioButton.setEnabled(false);
         }
     }

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/dynamic/DynamicClusteringCoefficientPanel.java

@@ -56,7 +56,7 @@ public class DynamicClusteringCoefficientPanel extends javax.swing.JPanel {
 
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController.getModel().isUndirected()) {
+        if (graphController.getGraphModel().isUndirected()) {
             directedRadioButton.setEnabled(false);
         }
     }

modules/StatisticsPluginUI/src/main/java/org/gephi/ui/statistics/plugin/dynamic/DynamicDegreePanel.java

@@ -56,7 +56,7 @@ public class DynamicDegreePanel extends javax.swing.JPanel {
 
         //Disable directed if the graph is undirecteds
         GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController.getModel().isUndirected()) {
+        if (graphController.getGraphModel().isUndirected()) {
             directedRadioButton.setEnabled(false);
         }
     }

modules/StatisticsPluginUI/src/main/resources/org/gephi/ui/statistics/plugin/Bundle.properties

@@ -2,24 +2,24 @@ OpenIDE-Module-Display-Category=Plugin
 OpenIDE-Module-Name=Statistics Plugin UI
 
 GraphDistancePanel.directedRadioButton.text=Directed
-GraphDistancePanel.undirectedRadioButton.text=UnDirected
+GraphDistancePanel.undirectedRadioButton.text=Undirected
 ClusteringCoefficientPanel.jLabel1.text=Clustering Coefficent Metric
 ClusteringCoefficientPanel.directedRadioButton.text=Directed
-ClusteringCoefficientPanel.undirectedRadioButton.text=UnDirected
+ClusteringCoefficientPanel.undirectedRadioButton.text=Undirected
 DegreeDistributionPanel.directedRadioButton.text=Directed
-DegreeDistributionPanel.undirectedRadioButton.text=UnDirected
+DegreeDistributionPanel.undirectedRadioButton.text=Undirected
 OpenIDE-Module-Short-Description=Standard statistics UI implementations
 PageRankPanel.probTextField.text=
 PageRankPanel.epsilonTextField.text=
 HitsPanel.epsilonTextField.text=
 GraphDensityPanel.directedRadioButton.text=Directed
-GraphDensityPanel.undirectedRadioButton.text=UnDirected
+GraphDensityPanel.undirectedRadioButton.text=Undirected
 DegreeDistributionPanel.descriptionLabel.text=
 GraphDistancePanel.descriptionLabel.text=
 HitsPanel.labelEpsilon.text=Epsilon:
 HitsPanel.descriptionLabel.text=
 HitsPanel.directedRadioButton.text=Directed
-HitsPanel.undirectedRadioButton.text=UnDirected
+HitsPanel.undirectedRadioButton.text=Undirected
 ModularityPanel.randomizeCheckbox.text=Randomize
 ModularityPanel.desriptionLabel.text=
 PageRankPanel.labelP.text=Probability (p):
@@ -50,7 +50,7 @@ PageRankPanel.jXLabel2.text=Stopping criterion, the smaller this value, the long
 ModularityPanel.header.title=Modularity
 ModularityPanel.header.description=Community detection algorithm.
 ConnectedComponentPanel.header.description=Determines the number of connected components in the network.
-ConnectedComponentPanel.undirectedRadioButton.text=UnDirected
+ConnectedComponentPanel.undirectedRadioButton.text=Undirected
 ConnectedComponentPanel.directedRadioButton.text=Directed
 ConnectedComponentPanel.header.title=Connected Components
 ConnectedComponentPanel.jLabel1.text=Detects strongly & weakly connected components
@@ -60,7 +60,7 @@ EigenvectorCentralityPanel.header.title=Eigenvector Centrality
 EigenvectorCentralityPanel.iterationsTextField.text=jTextField1
 EigenvectorCentralityPanel.labeliterations.text=Number of iterations:
 EigenvectorCentralityPanel.directedButton.text=Directed
-EigenvectorCentralityPanel.undirectedButton.text=UnDirected
+EigenvectorCentralityPanel.undirectedButton.text=Undirected
 GraphDistancePanel.normalizeButton.text=Normalize Centralities in [0,1]
 
 ConnectedComponentUI.name=Connected Components

modules/VisualizationImpl/pom.xml

@@ -75,12 +75,12 @@
         <dependency>
             <groupId>org.jogamp.gluegen</groupId>
             <artifactId>gluegen-rt-main</artifactId>
-            <version>2.1.1</version>
+            <version>2.1.3</version>
         </dependency>
         <dependency>
             <groupId>org.jogamp.jogl</groupId>
             <artifactId>jogl-all-main</artifactId>
-            <version>2.1.1</version>
+            <version>2.1.3</version>
         </dependency>
         <dependency>
             <groupId>org.netbeans.api</groupId>

modules/application/pom.xml

@@ -217,20 +217,20 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>spigot-plugin-ui</artifactId>
         </dependency>-->
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>statistics-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>statistics-plugin</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>statistics-plugin-ui</artifactId>
+        </dependency>
         <!--        <dependency>
-                    <groupId>${project.groupId}</groupId>
-                    <artifactId>statistics-api</artifactId>
-                </dependency>
-                <dependency>
-                    <groupId>${project.groupId}</groupId>
-                    <artifactId>statistics-plugin</artifactId>
-                </dependency>
-                <dependency>
-                    <groupId>${project.groupId}</groupId>
-                    <artifactId>statistics-plugin-ui</artifactId>
-                </dependency>
-                <dependency>
-                    <groupId>${project.groupId}</groupId>
+                     <groupId>${project.groupId}</groupId>
                     <artifactId>timeline</artifactId>
                 </dependency>
         -->        
@@ -302,11 +302,10 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>io-exporter-plugin</artifactId>
         </dependency>
-        <!--
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>desktop-statistics</artifactId>
-        </dependency>-->
+        </dependency>
         <!--        <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>filters-api</artifactId>

modules/application/src/main/resources/Info.plist

@@ -1,59 +1,59 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <plist version="1.0">
-  <dict>
+    <dict>
 
-    <key>CFBundleName</key>
-    <string>Gephi</string>
+        <key>CFBundleName</key>
+        <string>Gephi</string>
     
-    <key>CFBundleVersion</key>
-    <string>${project.version}</string>
+        <key>CFBundleVersion</key>
+        <string>${project.version}</string>
     
-    <key>CFBundleExecutable</key>
-    <string>gephi</string>
+        <key>CFBundleExecutable</key>
+        <string>gephi</string>
     
-    <key>CFBundlePackageType</key>
-    <string>APPL</string>
+        <key>CFBundlePackageType</key>
+        <string>APPL</string>
     
-    <key>CFBundleShortVersionString</key>
-    <string>${project.version}</string>
+        <key>CFBundleShortVersionString</key>
+        <string>${project.version}</string>
     
-    <key>CFBundleSignature</key>
-    <string>????</string>
+        <key>CFBundleSignature</key>
+        <string>????</string>
     
-    <key>CFBundleInfoDictionaryVersion</key>
-    <string>6.0</string>
+        <key>CFBundleInfoDictionaryVersion</key>
+        <string>6.0</string>
     
-    <key>CFBundleIdentifier</key>
-    <string>org.gephi</string>
+        <key>CFBundleIdentifier</key>
+        <string>org.gephi</string>
     
-    <key>CFBundleIconFile</key>
-    <string>gephi.icns</string>
+        <key>CFBundleIconFile</key>
+        <string>gephi.icns</string>
     
-    <key>NSHighResolutionCapable</key> 
-    <true/>
+        <key>NSHighResolutionCapable</key> 
+        <true/>
 	
-	<key>CFBundleDocumentTypes</key>
-    <array>
-      <dict>
-        <key>CFBundleTypeExtensions</key>
+        <key>CFBundleDocumentTypes</key>
         <array>
-          <string>gephi</string>
+            <dict>
+                <key>CFBundleTypeExtensions</key>
+                <array>
+                    <string>gephi</string>
+                </array>
+                <key>CFBundleTypeName</key>
+                <string>Gephi Project File</string>
+                <key>CFBundleTypeRole</key>
+                <string>Viewer</string>
+            </dict>
+            <dict>
+                <key>CFBundleTypeExtensions</key>
+                <array>
+                    <string>gexf</string>
+                </array>
+                <key>CFBundleTypeName</key>
+                <string>GEXF Graph File</string>
+                <key>CFBundleTypeRole</key>
+                <string>Viewer</string>
+            </dict>
         </array>
-        <key>CFBundleTypeName</key>
-        <string>Gephi Project File</string>
-        <key>CFBundleTypeRole</key>
-        <string>Viewer</string>
-      </dict>
-	  <dict>
-        <key>CFBundleTypeExtensions</key>
-        <array>
-          <string>gexf</string>
-        </array>
-        <key>CFBundleTypeName</key>
-        <string>GEXF Graph File</string>
-        <key>CFBundleTypeRole</key>
-        <string>Viewer</string>
-      </dict>
-    </array>
-  </dict>
+    </dict>
 </plist>

pom.xml

@@ -725,6 +725,16 @@
             </dependency>
         </dependencies>
     </dependencyManagement>
+    
+    <!-- TestNG dependency -->
+    <dependencies>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8.7</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
 
     <build>
         
@@ -1174,6 +1184,7 @@
         <module>modules/DesktopProgress</module>
         <module>modules/DesktopProject</module>
         <module>modules/DesktopRecentFiles</module>
+        <module>modules/DesktopStatistics</module>
         <module>modules/DirectoryChooser</module>
         <module>modules/DynamicAPI</module>
         <module>modules/ExportAPI</module>
@@ -1200,6 +1211,9 @@
         <module>modules/ProjectAPI</module>
         <module>modules/ProjectUI</module>
         <module>modules/SettingsUpgrader</module>
+        <module>modules/StatisticsAPI</module>
+        <module>modules/StatisticsPlugin</module>
+        <module>modules/StatisticsPluginUI</module>
         <module>modules/ToolsAPI</module>
         <module>modules/UIComponents</module>
         <module>modules/UIUtils</module>