Add Statistics modules and update implementations to use the new API

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/TimeFormat.java

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

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;
@@ -219,56 +230,59 @@ 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();
         }
     }
-
+    
     public double getAverageClusteringCoefficient() {
         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)
+        if (isDirected) {
             bruteForce(hgraph, attributeModel);
-        else
+        } else {
             triangles(hgraph);
-        
-
-        //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]);
+                }
             }
         }
     }
@@ -302,7 +316,6 @@ public class ClusteringCoefficient implements Statistics, LongTask {
             }
         }
 
-
         if (v > network[v].get(right)) {
             return (right);
         } else {
@@ -343,6 +356,7 @@ public class ClusteringCoefficient implements Statistics, LongTask {
             } else if (network[u].get(iu) > network[v].get(iv)) {
                 iv++;
             } else { /* neighbor in common */
+
                 w = network[u].get(iu);
                 if (w >= K) {
                     triangles[w] += count;
@@ -353,7 +367,7 @@ public class ClusteringCoefficient implements Statistics, LongTask {
         }
     }
 
-    public void triangles(HierarchicalGraph hgraph) {
+    public void triangles(Graph hgraph) {
 
         int ProgressCount = 0;
         Progress.start(progress, 7 * hgraph.getNodeCount());
@@ -363,10 +377,14 @@ public class ClusteringCoefficient implements Statistics, LongTask {
         N = hgraph.getNodeCount();
         nodeClustering = new double[N];
 
-        /** Create network for processing */
+        /**
+         * Create network for processing
+         */
         network = new ArrayWrapper[N];
 
-        /**  */
+        /**
+         *
+         */
         HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
         int index = 0;
         for (Node s : hgraph.getNodes()) {
@@ -381,18 +399,18 @@ public class ClusteringCoefficient implements Statistics, LongTask {
             HashMap<Node, EdgeWrapper> neighborTable = new HashMap<Node, EdgeWrapper>();
 
             if (!isDirected) {
-                for (Edge edge : hgraph.getEdgesAndMetaEdges(node)) {
+                for (Edge edge : hgraph.getEdges(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());
+                for (Edge in : ((DirectedGraph) hgraph).getInEdges(node)) {
+                    Node neighbor = in.getSource();
                     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());
+                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)]));
@@ -433,7 +451,6 @@ public class ClusteringCoefficient implements Statistics, LongTask {
         triangles = new int[N];
         K = (int) Math.sqrt(N);
 
-
         for (int v = 0; v < K && v < N; v++) {
             newVertex(v);
             Progress.progress(progress, ++ProgressCount);
@@ -484,72 +501,73 @@ public class ClusteringCoefficient implements Statistics, LongTask {
         hgraph.readUnlock();
     }
 
-    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));
-    }
-    
-    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;
-    }
-    if (isDirected) {
-    if (((HierarchicalDirectedGraph) hgraph).getEdge(neighbor1, neighbor2) != null) {
-    nodeCC++;
-    }
-    if (((HierarchicalDirectedGraph) hgraph).getEdge(neighbor2, neighbor1) != null) {
-    nodeCC++;
-    }
-    } 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 bruteForce(Graph hgraph, AttributeModel attributeModel) {
+        //The atrributes computed by the statistics
+        Table nodeTable = attributeModel.getNodeTable();
+        Column clusteringCol = nodeTable.getColumn("clustering");
+        if (clusteringCol == null) {
+            clusteringCol = nodeTable.addColumn("clustering", "Clustering Coefficient", Double.class, new Double(0));
+        }
+
+        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;
+                    }
+                    if (isDirected) {
+                        if (hgraph.isAdjacent(neighbor1, neighbor2)) {
+                            nodeCC++;
+                        }
+                        if (hgraph.isAdjacent(neighbor2, neighbor1)) {
+                            nodeCC++;
+                        }
+                    } 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));
+                }
+
+                node.setAttribute(clusteringCol, cc);
+
+                totalCC += cc;
+            }
+
+            if (isCanceled) {
+                break;
+            }
+
+            node_count++;
+            Progress.progress(progress, node_count);
+
+        }
+        avgClusteringCoeff = totalCC / hgraph.getNodeCount();
+
+        hgraph.readUnlockAll();
     }
+
+    @Override
     public String getReport() {
         //distribution of values
         Map<Double, Integer> dist = new HashMap<Double, Integer>();
@@ -584,20 +602,20 @@ 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 +628,7 @@ 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 +639,13 @@ 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

@@ -1,43 +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;
 
@@ -48,20 +48,17 @@ 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.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;
@@ -91,48 +88,51 @@ 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;
 
-        HierarchicalUndirectedGraph undirectedGraph = graphModel.getHierarchicalUndirectedGraphVisible();
+        UndirectedGraph undirectedGraph = graphModel.getUndirectedGraphVisible();
         weaklyConnected(undirectedGraph, attributeModel);
         if (isDirected) {
-            HierarchicalDirectedGraph directedGraph = graphModel.getHierarchicalDirectedGraphVisible();
+            DirectedGraph directedGraph = graphModel.getDirectedGraphVisible();
             top_tarjans(directedGraph, attributeModel);
         }
     }
 
-    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);
+
+        Table nodeTable = attributeModel.getNodeTable();
+        Column componentCol = nodeTable.getColumn(WEAKLY);
         if (componentCol == null) {
-            componentCol = nodeTable.addColumn(WEAKLY, "Component ID", AttributeType.INT, AttributeOrigin.COMPUTED, new Integer(0));
+            componentCol = nodeTable.addColumn(WEAKLY, "Component ID", Integer.class, new Integer(0));
         }
 
         List<Integer> sizeList = new ArrayList<Integer>();
 
-        hgraph.readLock();
+        graph.readLock();
 
         HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
         int index = 0;
-        for (Node s : hgraph.getNodes()) {
+        for (Node s : graph.getNodes()) {
             indicies.put(s, index);
             index++;
         }
 
-
-        int N = hgraph.getNodeCount();
+        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, graph.getNodeCount());
         int seenCount = 0;
         while (seenCount < N) {
             //The search Q
@@ -141,7 +141,7 @@ 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);
@@ -153,7 +153,7 @@ public class ConnectedComponents implements Statistics, LongTask {
             //While there are more nodes to search
             while (!Q.isEmpty()) {
                 if (isCanceled) {
-                    hgraph.readUnlock();
+                    graph.readUnlock();
                     return;
                 }
                 //Get the next Node and add it to the component list
@@ -161,11 +161,11 @@ public class ConnectedComponents implements Statistics, LongTask {
                 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) {
@@ -181,13 +181,12 @@ public class ConnectedComponents implements Statistics, LongTask {
                 seenCount++;
             }
             for (Node s : component) {
-                AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
-                row.setValue(componentCol, componentCount);
+                s.setAttribute(componentCol, componentCount);
             }
             sizeList.add(component.size());
             componentCount++;
         }
-        hgraph.readUnlock();
+        graph.readUnlock();
 
         componentsSize = new int[sizeList.size()];
         for (int i = 0; i < sizeList.size(); i++) {
@@ -195,24 +194,24 @@ public class ConnectedComponents implements Statistics, LongTask {
         }
     }
 
-    public void top_tarjans(HierarchicalDirectedGraph hgraph, AttributeModel attributeModel) {
+    public void top_tarjans(DirectedGraph graph, AttributeModel attributeModel) {
         count = 1;
         stronglyCount = 0;
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn componentCol = nodeTable.getColumn(STRONG);
+        Table nodeTable = attributeModel.getNodeTable();
+        Column componentCol = nodeTable.getColumn(STRONG);
         if (componentCol == null) {
-            componentCol = nodeTable.addColumn(STRONG, "Strongly-Connected ID", AttributeType.INT, AttributeOrigin.COMPUTED, new Integer(0));
+            componentCol = nodeTable.addColumn(STRONG, "Strongly-Connected ID", Integer.class, new Integer(0));
         }
 
-        hgraph.readLock();
+        graph.readLock();
 
         HashMap<Node, Integer> indicies = new HashMap<Node, Integer>();
         int v = 0;
-        for (Node s : hgraph.getNodes()) {
+        for (Node s : graph.getNodes()) {
             indicies.put(s, v);
             v++;
         }
-        int N = hgraph.getNodeCount();
+        int N = graph.getNodeCount();
         int[] index = new int[N];
         int[] low_index = new int[N];
 
@@ -223,7 +222,7 @@ 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;
@@ -232,25 +231,25 @@ public class ConnectedComponents implements Statistics, LongTask {
                 }
             }
             if (first == null) {
-                hgraph.readUnlockAll();
+                graph.readUnlockAll();
                 return;
             }
-            tarjans(componentCol, S, hgraph, first, index, low_index, indicies);
+            tarjans(componentCol, S, graph, 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 void tarjans(Column col, 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(col, 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]);
@@ -260,8 +259,7 @@ public class ConnectedComponents implements Statistics, LongTask {
             Node v = null;
             while (v != f) {
                 v = S.removeFirst();
-                AttributeRow row = (AttributeRow) v.getNodeData().getAttributes();
-                row.setValue(col, stronglyCount);
+                v.setAttribute(col, stronglyCount);
             }
             stronglyCount++;
         }
@@ -296,15 +294,16 @@ public class ConnectedComponents implements Statistics, LongTask {
         return maxIndex;
     }
 
+    @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 +326,6 @@ 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 +334,7 @@ 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 +342,13 @@ 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

@@ -45,16 +45,13 @@ 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.Column;
+import org.gephi.attribute.api.Origin;
+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;
@@ -96,58 +93,47 @@ 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);
+        Table nodeTable = attributeModel.getNodeTable();
+        Column inCol = nodeTable.getColumn(INDEGREE);
+        Column outCol = nodeTable.getColumn(OUTDEGREE);
+        Column degCol = nodeTable.getColumn(DEGREE);
+
         if (isDirected) {
             if (inCol == null) {
-                inCol = nodeTable.addColumn(INDEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.InDegree"), AttributeType.INT, AttributeOrigin.COMPUTED, 0);
+                inCol = nodeTable.addColumn(INDEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.InDegree"), Integer.class, 0);
             }
             if (outCol == null) {
-                outCol = nodeTable.addColumn(OUTDEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.OutDegree"), AttributeType.INT, AttributeOrigin.COMPUTED, 0);
+                outCol = nodeTable.addColumn(OUTDEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.OutDegree"), Integer.class, 0);
             }
         }
         if (degCol == null) {
-            degCol = nodeTable.addColumn(DEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.Degree"), AttributeType.INT, AttributeOrigin.COMPUTED, 0);
+            degCol = nodeTable.addColumn(DEGREE, NbBundle.getMessage(Degree.class, "Degree.nodecolumn.Degree"), Integer.class, 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;
 
         graph.readLock();
-
-        Progress.start(progress, graph.getNodeCount());
         
-        HierarchicalDirectedGraph directedGraph = null;
-        if(isDirected) {
-            directedGraph = graph.getGraphModel().getHierarchicalDirectedGraphVisible();
-        }
+        Progress.start(progress, graph.getNodeCount());
 
         for (Node n : graph.getNodes()) {
-            AttributeRow row = (AttributeRow) n.getNodeData().getAttributes();
             if (isDirected) {
-                int inDegree = directedGraph.getTotalInDegree(n);
-                int outDegree = directedGraph.getTotalOutDegree(n);
-                row.setValue(inCol, inDegree);
-                row.setValue(outCol, outDegree);
+                int inDegree = ((DirectedGraph)graph).getInDegree(n);
+                int outDegree = ((DirectedGraph)graph).getOutDegree(n);
+                n.setAttribute(inCol, inDegree);
+                n.setAttribute(outCol, outDegree);
                 if (!inDegreeDist.containsKey(inDegree)) {
                     inDegreeDist.put(inDegree, 0);
                 }
@@ -157,8 +143,8 @@ public class Degree implements Statistics, LongTask {
                 }
                 outDegreeDist.put(outDegree, outDegreeDist.get(outDegree) + 1);
             }
-            int degree = graph.getTotalDegree(n);
-            row.setValue(degCol, degree);
+            int degree = graph.getDegree(n);
+            n.setAttribute(degCol, degree);
             avgDegree += degree;
             if (!degreeDist.containsKey(degree)) {
                 degreeDist.put(degree, 0);
@@ -168,20 +154,22 @@ public class Degree implements Statistics, LongTask {
             if (isCanceled) {
                 break;
             }
-            i++;
-            Progress.progress(progress, i);
+            Progress.progress(progress);
         }
 
         avgDegree /= graph.getNodeCount();
-        graph.getAttributes().setValue(avgDegreeCol.getIndex(), avgDegree);
+        graph.setAttribute(AVERAGE_DEGREE, avgDegree);
 
         graph.readUnlockAll();
+        
+        Progress.finish(progress);
     }
 
     /**
      *
      * @return
      */
+    @Override
     public String getReport() {
         String report = "";
         if (isDirected) {
@@ -294,6 +282,7 @@ public class Degree implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public boolean cancel() {
         this.isCanceled = true;
         return true;
@@ -303,6 +292,7 @@ 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;
@@ -79,23 +75,24 @@ 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();
         }
     }
-
+    
     public void setNumRuns(int numRuns) {
         this.numRuns = numRuns;
     }
 
     /**
-     * 
+     *
      * @return
      */
     public int getNumRuns() {
@@ -103,7 +100,7 @@ public class EigenvectorCentrality implements Statistics, LongTask {
     }
 
     /**
-     * 
+     *
      * @return
      */
     public boolean isDirected() {
@@ -111,7 +108,7 @@ public class EigenvectorCentrality implements Statistics, LongTask {
     }
 
     /**
-     * 
+     *
      * @param isDirected
      */
     public void setDirected(boolean isDirected) {
@@ -123,22 +120,26 @@ 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);
+        Table nodeTable = attributeModel.getNodeTable();
+        Column eigenCol = nodeTable.getColumn(EIGENVECTOR);
         if (eigenCol == null) {
-            eigenCol = nodeTable.addColumn(EIGENVECTOR, "Eigenvector Centrality", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
+            eigenCol = nodeTable.addColumn(EIGENVECTOR, "Eigenvector Centrality", Double.class, new Double(0));
         }
 
         int N = hgraph.getNodeCount();
@@ -164,9 +165,9 @@ public class EigenvectorCentrality implements Statistics, LongTask {
                 Node u = indicies.get(i);
                 EdgeIterable iter = null;
                 if (isDirected) {
-                    iter = ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(u);
+                    iter = ((DirectedGraph) hgraph).getInEdges(u);
                 } else {
-                    iter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(u);
+                    iter = hgraph.getEdges(u);
                 }
 
                 for (Edge e : iter) {
@@ -199,8 +200,7 @@ public class EigenvectorCentrality implements Statistics, LongTask {
 
         for (int i = 0; i < N; i++) {
             Node s = indicies.get(i);
-            AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
-            row.setValue(eigenCol, centralities[i]);
+            s.setAttribute(eigenCol, centralities[i]);
             if (isCanceled) {
                 return;
             }
@@ -211,9 +211,10 @@ public class EigenvectorCentrality implements Statistics, LongTask {
     }
 
     /**
-     * 
+     *
      * @return
      */
+    @Override
     public String getReport() {
         //distribution of values
         Map<Double, Integer> dist = new HashMap<Double, Integer>();
@@ -246,7 +247,7 @@ 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 +262,13 @@ 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

@@ -43,12 +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.graph.api.GraphController;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphModel;
-import org.gephi.graph.api.HierarchicalGraph;
 import org.gephi.statistics.spi.Statistics;
-import org.openide.util.Lookup;
 
 /**
  *
@@ -61,13 +59,6 @@ public class GraphDensity implements Statistics {
     /** */
     private boolean isDirected;
 
-    public GraphDensity() {
-        GraphController graphController = Lookup.getDefault().lookup(GraphController.class);
-        if (graphController != null && graphController.getModel() != null) {
-            isDirected = graphController.getModel().isDirected();
-        }
-    }
-
     public void setDirected(boolean isDirected) {
         this.isDirected = isDirected;
     }
@@ -80,17 +71,19 @@ public class GraphDensity implements Statistics {
         return density;
     }
 
+    @Override
     public void execute(GraphModel graphModel, AttributeModel attributeModel) {
-        HierarchicalGraph hgraph;
+        isDirected = graphModel.isDirected();
 
+        Graph graph;
         if (isDirected) {
-            hgraph = graphModel.getHierarchicalDirectedGraphVisible();
+            graph = graphModel.getDirectedGraphVisible();
         } else {
-            hgraph = graphModel.getHierarchicalUndirectedGraphVisible();
+            graph = graphModel.getUndirectedGraphVisible();
         }
 
-        double edgesCount = hgraph.getTotalEdgeCount();
-        double nodesCount = hgraph.getNodeCount();
+        double edgesCount = graph.getEdgeCount();
+        double nodesCount = graph.getNodeCount();
         double multiplier = 1;
 
         if (!isDirected) {
@@ -103,6 +96,7 @@ public class GraphDensity implements Statistics {
      *
      * @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;
@@ -69,8 +66,8 @@ import org.openide.util.Exceptions;
 import org.openide.util.Lookup;
 
 /**
- * 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
  */
@@ -79,75 +76,88 @@ 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 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);
+        Table nodeTable = attributeModel.getNodeTable();
+        Column eccentricityCol = nodeTable.getColumn(ECCENTRICITY);
+        Column closenessCol = nodeTable.getColumn(CLOSENESS);
+        Column betweenessCol = nodeTable.getColumn(BETWEENNESS);
         if (eccentricityCol == null) {
-            eccentricityCol = nodeTable.addColumn(ECCENTRICITY, "Eccentricity", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
+            eccentricityCol = nodeTable.addColumn(ECCENTRICITY, "Eccentricity", Double.class, new Double(0));
         }
         if (closenessCol == null) {
-            closenessCol = nodeTable.addColumn(CLOSENESS, "Closeness Centrality", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
+            closenessCol = nodeTable.addColumn(CLOSENESS, "Closeness Centrality", Double.class, new Double(0));
         }
         if (betweenessCol == null) {
-            betweenessCol = nodeTable.addColumn(BETWEENNESS, "Betweenness Centrality", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
+            betweenessCol = nodeTable.addColumn(BETWEENNESS, "Betweenness Centrality", Double.class, new Double(0));
         }
 
         hgraph.readLock();
@@ -196,9 +206,9 @@ public class GraphDistance implements Statistics, LongTask {
 
                 EdgeIterable edgeIter = null;
                 if (isDirected) {
-                    edgeIter = ((HierarchicalDirectedGraph) hgraph).getOutEdgesAndMetaOutEdges(v);
+                    edgeIter = ((DirectedGraph) hgraph).getOutEdges(v);
                 } else {
-                    edgeIter = hgraph.getEdgesAndMetaEdges(v);
+                    edgeIter = hgraph.getEdges(v);
                 }
 
                 for (Edge edge : edgeIter) {
@@ -259,7 +269,6 @@ public class GraphDistance implements Statistics, LongTask {
         avgDist /= shortestPaths;//mN * (mN - 1.0f);
 
         for (Node s : hgraph.getNodes()) {
-            AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
             int s_index = indicies.get(s);
 
             if (!isDirected) {
@@ -269,9 +278,9 @@ public class GraphDistance implements Statistics, LongTask {
                 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(eccentricityCol, eccentricity[s_index]);
+            s.setAttribute(closenessCol, closeness[s_index]);
+            s.setAttribute(betweenessCol, betweenness[s_index]);
         }
         hgraph.readUnlock();
     }
@@ -330,6 +339,7 @@ public class GraphDistance implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public String getReport() {
         String htmlIMG1 = "";
         String htmlIMG2 = "";
@@ -364,9 +374,10 @@ public class GraphDistance implements Statistics, LongTask {
     }
 
     /**
-     * 
+     *
      * @return
      */
+    @Override
     public boolean cancel() {
         this.isCanceled = true;
         return true;
@@ -376,6 +387,7 @@ 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

@@ -1,62 +1,58 @@
 /*
-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.statistics.spi.Statistics;
 import org.gephi.utils.longtask.spi.LongTask;
@@ -70,8 +66,8 @@ 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
  */
@@ -91,8 +87,8 @@ public class Hits implements Statistics, LongTask {
 
     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();
         }
     }
 
@@ -101,24 +97,25 @@ 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) {
         hgraph.readLock();
 
         int N = hgraph.getNodeCount();
@@ -139,21 +136,20 @@ public class Hits implements Statistics, LongTask {
             index++;
 
             if (!useUndirected) {
-                if (((HierarchicalDirectedGraph) hgraph).getTotalOutDegree(node) > 0) {
+                if (((DirectedGraph) hgraph).getOutDegree(node) > 0) {
                     hub_list.add(node);
                 }
-                if (((HierarchicalDirectedGraph) hgraph).getTotalInDegree(node) > 0) {
+                if (((DirectedGraph) hgraph).getInDegree(node) > 0) {
                     auth_list.add(node);
                 }
             } else {
-                if (((HierarchicalUndirectedGraph) hgraph).getTotalDegree(node) > 0) {
+                if (hgraph.getDegree(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;
@@ -173,9 +169,9 @@ public class Hits implements Statistics, LongTask {
                 temp_authority[n_index] = authority[n_index];
                 EdgeIterable edge_iter;
                 if (!useUndirected) {
-                    edge_iter = ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(node);
+                    edge_iter = ((DirectedGraph) hgraph).getInEdges(node);
                 } else {
-                    edge_iter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(node);
+                    edge_iter = hgraph.getEdges(node);
                 }
                 for (Edge edge : edge_iter) {
                     Node target = hgraph.getOpposite(node, edge);
@@ -197,9 +193,9 @@ public class Hits implements Statistics, LongTask {
                 temp_hubs[n_index] = hubs[n_index];
                 EdgeIterable edge_iter;
                 if (!useUndirected) {
-                    edge_iter = ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(node);
+                    edge_iter = ((DirectedGraph) hgraph).getInEdges(node);
                 } else {
-                    edge_iter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(node);
+                    edge_iter = hgraph.getEdges(node);
                 }
                 for (Edge edge : edge_iter) {
                     Node target = hgraph.getOpposite(node, edge);
@@ -227,7 +223,6 @@ public class Hits implements Statistics, LongTask {
                 }
             }
 
-
             authority = temp_authority;
             hubs = temp_hubs;
             temp_authority = new double[N];
@@ -238,21 +233,20 @@ public class Hits implements Statistics, LongTask {
             }
         }
 
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn authorityCol = nodeTable.getColumn(AUTHORITY);
-        AttributeColumn hubsCol = nodeTable.getColumn(HUB);
+        Table nodeTable = attributeModel.getNodeTable();
+        Column authorityCol = nodeTable.getColumn(AUTHORITY);
+        Column hubsCol = nodeTable.getColumn(HUB);
         if (authorityCol == null) {
-            authorityCol = nodeTable.addColumn(AUTHORITY, "Authority", AttributeType.FLOAT, AttributeOrigin.COMPUTED, new Float(0));
+            authorityCol = nodeTable.addColumn(AUTHORITY, "Authority", Float.class, new Float(0));
         }
         if (hubsCol == null) {
-            hubsCol = nodeTable.addColumn(HUB, "Hub", AttributeType.FLOAT, AttributeOrigin.COMPUTED, new Float(0));
+            hubsCol = nodeTable.addColumn(HUB, "Hub", Float.class, new Float(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]);
+            s.setAttribute(authorityCol, (float) authority[s_index]);
+            s.setAttribute(hubsCol, (float) hubs[s_index]);
         }
 
         hgraph.readUnlockAll();
@@ -262,6 +256,7 @@ public class Hits implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public String getReport() {
         //distribution of hub values
         Map<Double, Integer> distHubs = new HashMap<Double, Integer>();
@@ -329,7 +324,6 @@ 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 +341,7 @@ public class Hits implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public boolean cancel() {
         isCanceled = true;
         return true;
@@ -356,6 +351,7 @@ 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;
@@ -449,12 +448,13 @@ 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;
         Progress.start(progress);
         Random rand = new Random();
@@ -483,12 +483,12 @@ public class Modularity implements Statistics, LongTask {
                     Community bestCommunity = null;
                     Community nodecom = structure.nodeCommunities[i];
                     Set<Community> iter = structure.nodeConnectionsWeight[i].keySet();
-                    for(Community com : iter) {
+                    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);
@@ -525,40 +525,39 @@ public class Modularity implements Statistics, LongTask {
         }
         for (Node node : hgraph.getNodes()) {
             int index = structure.map.get(node);
-            if(useWeight) {
+            if (useWeight) {
                 degreeCount[comStructure[index]] += nodeDegrees[index];
-            } else {                
-                degreeCount[comStructure[index]] += hgraph.getTotalDegree(node);
+            } else {
+                degreeCount[comStructure[index]] += hgraph.getDegree(node);
             }
-            
+
         }
-        
+
         modularity = finalQ(comStructure, degreeCount, hgraph, attributeModel, totalWeight, 1.);
         modularityResolution = finalQ(comStructure, degreeCount, hgraph, attributeModel, totalWeight, resolution);
-        
+
         hgraph.readUnlock();
     }
 
-    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);
+    private double finalQ(int[] struct, double[] degrees, Graph hgraph, AttributeModel attributeModel, double totalWeight, double usedResolution) {
+        Table nodeTable = attributeModel.getNodeTable();
+        Column modCol = nodeTable.getColumn(MODULARITY_CLASS);
         if (modCol == null) {
-            modCol = nodeTable.addColumn(MODULARITY_CLASS, "Modularity Class", AttributeType.INT, AttributeOrigin.COMPUTED, new Integer(0));
+            modCol = nodeTable.addColumn(MODULARITY_CLASS, "Modularity Class", Integer.class, new Integer(0));
         }
 
         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]);
+            n.setAttribute(modCol, struct[n_index]);
             for (Node neighbor : hgraph.getNeighbors(n)) {
                 if (n == neighbor) {
                     continue;
                 }
                 int neigh_index = structure.map.get(neighbor);
                 if (struct[neigh_index] == struct[n_index]) {
-                    if(useWeight) {
+                    if (useWeight) {
                         internal[struct[neigh_index]] += hgraph.getEdge(n, neighbor).getWeight();
                     } else {
                         internal[struct[neigh_index]]++;
@@ -577,17 +576,18 @@ public class Modularity implements Statistics, LongTask {
         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 +607,19 @@ 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>"

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 +66,39 @@ 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();
         }
     }
 
@@ -110,17 +114,18 @@ 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;
 
         hgraph.readLock();
@@ -144,9 +149,9 @@ public class PageRank implements Statistics, LongTask {
                 double sum = 0;
                 EdgeIterable eIter;
                 if (isDirected) {
-                    eIter = ((HierarchicalDirectedGraph) hgraph).getOutEdgesAndMetaOutEdges(s);
+                    eIter = ((DirectedGraph) hgraph).getOutEdges(s);
                 } else {
-                    eIter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(s);
+                    eIter = ((UndirectedGraph) hgraph).getEdges(s);
                 }
                 for (Edge edge : eIter) {
                     sum += edge.getWeight();
@@ -162,9 +167,9 @@ public class PageRank implements Statistics, LongTask {
                 int s_index = indicies.get(s);
                 boolean out;
                 if (isDirected) {
-                    out = ((HierarchicalDirectedGraph) hgraph).getTotalOutDegree(s) > 0;
+                    out = ((DirectedGraph) hgraph).getOutDegree(s) > 0;
                 } else {
-                    out = hgraph.getTotalDegree(s) > 0;
+                    out = hgraph.getDegree(s) > 0;
                 }
 
                 if (out) {
@@ -185,9 +190,9 @@ public class PageRank implements Statistics, LongTask {
 
                 EdgeIterable eIter;
                 if (isDirected) {
-                    eIter = ((HierarchicalDirectedGraph) hgraph).getInEdgesAndMetaInEdges(s);
+                    eIter = ((DirectedGraph) hgraph).getInEdges(s);
                 } else {
-                    eIter = ((HierarchicalUndirectedGraph) hgraph).getEdgesAndMetaEdges(s);
+                    eIter = hgraph.getEdges(s);
                 }
 
                 for (Edge edge : eIter) {
@@ -195,9 +200,9 @@ public class PageRank implements Statistics, LongTask {
                     int neigh_index = indicies.get(neighbor);
                     int normalize;
                     if (isDirected) {
-                        normalize = ((HierarchicalDirectedGraph) hgraph).getTotalOutDegree(neighbor);
+                        normalize = ((DirectedGraph) hgraph).getOutDegree(neighbor);
                     } else {
-                        normalize = ((HierarchicalUndirectedGraph) hgraph).getTotalDegree(neighbor);
+                        normalize = hgraph.getDegree(neighbor);
                     }
                     if (useEdgeWeight) {
                         double weight = edge.getWeight() / weights[neigh_index];
@@ -226,16 +231,15 @@ public class PageRank implements Statistics, LongTask {
 
         }
 
-        AttributeTable nodeTable = attributeModel.getNodeTable();
-        AttributeColumn pangeRanksCol = nodeTable.getColumn(PAGERANK);
+        Table nodeTable = attributeModel.getNodeTable();
+        Column pangeRanksCol = nodeTable.getColumn(PAGERANK);
         if (pangeRanksCol == null) {
-            pangeRanksCol = nodeTable.addColumn(PAGERANK, "PageRank", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, new Double(0));
+            pangeRanksCol = nodeTable.addColumn(PAGERANK, "PageRank", Double.class, new Double(0));
         }
 
         for (Node s : hgraph.getNodes()) {
             int s_index = indicies.get(s);
-            AttributeRow row = (AttributeRow) s.getNodeData().getAttributes();
-            row.setValue(pangeRanksCol, pageranks[s_index]);
+            s.setAttribute(pangeRanksCol, pageranks[s_index]);
         }
 
         hgraph.readUnlockAll();
@@ -245,6 +249,7 @@ public class PageRank implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public String getReport() {
         //distribution of values
         Map<Double, Integer> dist = new HashMap<Double, Integer>();
@@ -277,7 +282,7 @@ 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 +302,7 @@ public class PageRank implements Statistics, LongTask {
      *
      * @return
      */
+    @Override
     public boolean cancel() {
         isCanceled = true;
         return true;
@@ -306,6 +312,7 @@ 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.graph.api.DirectedGraph;
+import org.gephi.attribute.api.AttributeModel;
+import org.gephi.attribute.api.Column;
+import org.gephi.attribute.api.Table;
 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;
@@ -89,31 +84,32 @@ 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);
+        Table nodeTable = attributeModel.getNodeTable();
+        Column degCol = nodeTable.getColumn(WDEGREE);
+        Column inCol = nodeTable.getColumn(WINDEGREE);
+        Column outCol = nodeTable.getColumn(WOUTDEGREE);
         if (degCol == null) {
-            degCol = nodeTable.addColumn(WDEGREE, "Weighted Degree", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, 0.0);
+            degCol = nodeTable.addColumn(WDEGREE, "Weighted Degree", Double.class, 0.0);
         }
         if (isDirected) {
             if (inCol == null) {
-                inCol = nodeTable.addColumn(WINDEGREE, "Weighted In-Degree", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, 0.0);
+                inCol = nodeTable.addColumn(WINDEGREE, "Weighted In-Degree", Double.class, 0.0);
             }
             if (outCol == null) {
-                outCol = nodeTable.addColumn(WOUTDEGREE, "Weighted Out-Degree", AttributeType.DOUBLE, AttributeOrigin.COMPUTED, 0.0);
+                outCol = nodeTable.addColumn(WOUTDEGREE, "Weighted Out-Degree", Double.class, 0.0);
             }
         }
 
@@ -123,24 +119,22 @@ public class WeightedDegree implements Statistics, LongTask {
         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();) {
+                for (Iterator it = graph.getEdges(n).iterator(); it.hasNext();) {
                     Edge e = (Edge) it.next();
-                    if (e.getSource().getNodeData().equals(n.getNodeData())) {
+                    if (e.getSource().equals(n)) {
                         totalOutWeight += e.getWeight();
                     }
-                    if (e.getTarget().getNodeData().equals(n.getNodeData())) {
+                    if (e.getTarget().equals(n)) {
                         totalInWeight += e.getWeight();
                     }
                 }
                 totalWeight = totalInWeight + totalOutWeight;
-                row.setValue(inCol, totalInWeight);
-                row.setValue(outCol, totalOutWeight);
+                n.setAttribute(inCol, totalInWeight);
+                n.setAttribute(outCol, totalOutWeight);
                 if (!inDegreeDist.containsKey(totalInWeight)) {
                     inDegreeDist.put(totalInWeight, 0);
                 }
@@ -150,13 +144,13 @@ public class WeightedDegree implements Statistics, LongTask {
                 }
                 outDegreeDist.put(totalOutWeight, outDegreeDist.get(totalOutWeight) + 1);
             } else {
-                for (Iterator it = graph.getEdgesAndMetaEdges(n).iterator(); it.hasNext();) {
+                for (Iterator it = graph.getEdges(n).iterator(); it.hasNext();) {
                     Edge e = (Edge) it.next();
                     totalWeight += e.getWeight();
                 }
             }
 
-            row.setValue(degCol, totalWeight);
+            n.setAttribute(degCol, totalWeight);
             avgWDegree += totalWeight;
 
             if (!degreeDist.containsKey(totalWeight)) {
@@ -176,6 +170,7 @@ public class WeightedDegree implements Statistics, LongTask {
         graph.readUnlockAll();
     }
 
+    @Override
     public String getReport() {
         String report = "";
 
@@ -282,11 +277,13 @@ 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/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/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>

pom.xml

@@ -1174,6 +1174,7 @@
         <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 +1201,9 @@
         <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>