Merge lp:~mathieu-jacomy/gephi/forceatlas2-multithread into lp:~gephi.team/gephi/0.8

[Mathieu Bastian]

Multithread version of ForceAtlas2

[lp:~mathieu-jacomy/gephi/forceatlas2-multithread]

2260. By Mathieu Jacomy on 2011-07-28

ForceAtlas2 Multithread - better strategy. Tested and working.

2261. By Mathieu Jacomy on 2011-08-30

Better ThreadPool implementation, added strong gravity

Unmerged revisions

2261. By Mathieu Jacomy on 2011-08-30

Better ThreadPool implementation, added strong gravity

2260. By Mathieu Jacomy on 2011-07-28

ForceAtlas2 Multithread - better strategy. Tested and working.

2259. By Mathieu Jacomy on 2011-07-26

ForceAtlas2 Multithreading (basic implementation: consumer-producer paradigm)

=== modified file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Bundle.properties'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Bundle.properties	2011-06-05 21:30:01 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Bundle.properties	2011-08-30 14:28:25 +0000
@@ -4,11 +4,14 @@
 ForceAtlas2.tuning=Tuning
 ForceAtlas2.behavior=Behavior Alternatives
 ForceAtlas2.performance=Performance
+ForceAtlas2.threads=Threads
 
 ForceAtlas2.scalingRatio.name=Scaling
 ForceAtlas2.scalingRatio.desc=How much repulsion you want. More makes a more sparse graph.
 ForceAtlas2.gravity.name=Gravity
 ForceAtlas2.gravity.desc=Attracts nodes to the center. Prevents islands from drifting away.
+ForceAtlas2.strongGravityMode.name=Stronger Gravity
+ForceAtlas2.strongGravityMode.desc=A stronger gravity law
 ForceAtlas2.distributedAttraction.name=Dissuade Hubs
 ForceAtlas2.distributedAttraction.desc=Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.
 ForceAtlas2.linLogMode.name=LinLog mode
@@ -23,3 +26,5 @@
 ForceAtlas2.barnesHutTheta.desc=Theta of the Barnes Hut optimization.
 ForceAtlas2.edgeWeightInfluence.name=Edge Weight Influence
 ForceAtlas2.edgeWeightInfluence.desc=How much influence you give to the edges weight. 0 is "no influence" and 1 is "normal".
+ForceAtlas2.threads.name=Threads number
+ForceAtlas2.threads.desc=More threads means more speed if your cores can handle it.
 
=== modified file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Bundle_fr.properties'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Bundle_fr.properties	2011-06-05 21:30:01 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Bundle_fr.properties	2011-08-30 14:28:25 +0000
@@ -4,11 +4,14 @@
 ForceAtlas2.tuning=R\u00e9glages fins
 ForceAtlas2.behavior=Options de comportement
 ForceAtlas2.performance=Performances
+ForceAtlas2.threads=Processus
 
 ForceAtlas2.scalingRatio.name=Dimensionnement
 ForceAtlas2.scalingRatio.desc=Quantit\u00e9 de r\u00e9pulsion, par rapport \u00e0 l'attraction. Rend le graphe plus \u00e9tal\u00e9.
 ForceAtlas2.gravity.name=Gravit\u00e9
 ForceAtlas2.gravity.desc=Attire les noeuds vers le centre. Emp\u00eache les \u00eelots de d\u00e9river \u00e0 l'infini.
+ForceAtlas2.strongGravityMode.name=Forte Gravit\u00e9
+ForceAtlas2.strongGravityMode.desc=Une loi de gravit\u00e9 plus forte
 ForceAtlas2.distributedAttraction.name=Dissuader les Hubs
 ForceAtlas2.distributedAttraction.desc=Distribue l'attraction dans les liens sortants. Les Hubs attirent moins et sont donc repouss\u00e9s en p\u00e9riph\u00e9rie.
 ForceAtlas2.linLogMode.name=Mode LinLog
@@ -23,3 +26,5 @@
 ForceAtlas2.barnesHutTheta.desc=param\u00e8tre Theta de l'optimisation de Barnes Hut.
 ForceAtlas2.edgeWeightInfluence.name=Influence Poids des liens
 ForceAtlas2.edgeWeightInfluence.desc=L'influence du poides des liens. 0 c'est aucune influence, 1 c'est une influence normale et au-del\u00e0 \u00e7a accentue l'importance du poids des liens dans la spatialisation.
+ForceAtlas2.threads.name=Nb. processus
+ForceAtlas2.threads.desc=Plus de processus multiplient les performances si vos processeurs peuvent les supporter.
 
=== modified file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/ForceAtlas2.java'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/ForceAtlas2.java	2011-06-05 21:30:01 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/ForceAtlas2.java	2011-08-30 14:28:25 +0000
@@ -22,6 +22,10 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
 import org.gephi.data.attributes.type.TimeInterval;
 import org.gephi.dynamic.DynamicUtilities;
 import org.gephi.dynamic.api.DynamicController;
@@ -37,6 +41,7 @@
 import org.gephi.layout.spi.LayoutBuilder;
 import org.gephi.layout.spi.LayoutProperty;
 import org.gephi.project.api.Workspace;
+import org.openide.util.Exceptions;
 import org.openide.util.Lookup;
 import org.openide.util.NbBundle;
 
@@ -60,10 +65,13 @@
     private boolean barnesHutOptimize;
     private double barnesHutTheta;
     private boolean linLogMode;
+    private boolean strongGravityMode;
+    private int threadCount;
     private Region rootRegion;
     double outboundAttCompensation = 1;
     //Dynamic Weight
     private TimeInterval timeInterval;
+    private ExecutorService pool;
 
     public ForceAtlas2(ForceAtlas2Builder layoutBuilder) {
         this.layoutBuilder = layoutBuilder;
@@ -93,6 +101,9 @@
             nLayout.dx = 0;
             nLayout.dy = 0;
         }
+        
+        pool = Executors.newFixedThreadPool(threadCount); 
+        
     }
 
     @Override
@@ -140,33 +151,45 @@
             outboundAttCompensation /= nodes.length;
         }
 
-        // Repulsion
+        // Repulsion (and gravity)
+        // NB: Muti-threaded
         RepulsionForce Repulsion = ForceFactory.builder.buildRepulsion(isAdjustSizes(), getScalingRatio());
-        if (isBarnesHutOptimize()) {
-            for (Node n : nodes) {
-                rootRegion.applyForce(n, Repulsion, getBarnesHutTheta());
-            }
-        } else {
-            for (int n1Index = 0; n1Index < nodes.length; n1Index++) {
-                Node n1 = nodes[n1Index];
-                for (int n2Index = 0; n2Index < n1Index; n2Index++) {
-                    Node n2 = nodes[n2Index];
-                    Repulsion.apply(n1, n2);
-                }
-            }
-        }
-
+        
+        int taskCount = 8*threadCount;  // The threadPool Executor Service will manage the fetching of tasks and threads.
+                                        // We make more tasks than threads because some tasks may need more time to compute.
+        ArrayList<Future> threads = new ArrayList();
+        for(int t=taskCount; t>0; t--){
+            int from = (int) Math.floor(nodes.length*(t-1)/taskCount);
+            int to = (int) Math.floor(nodes.length*t/taskCount);
+            Future future = pool.submit(new NodesThread(nodes, from, to, isBarnesHutOptimize(), getBarnesHutTheta(), getGravity(), (isStrongGravityMode())?(ForceFactory.builder.getStrongGravity(getScalingRatio())):(Repulsion), getScalingRatio(), rootRegion, Repulsion));
+            threads.add(future);
+        }
+        for(Future future : threads) {
+            try {
+                future.get();
+            } catch (InterruptedException ex) {
+                Exceptions.printStackTrace(ex);
+            } catch (ExecutionException ex) {
+                Exceptions.printStackTrace(ex);
+            }
+        }
+        
         // Attraction
         AttractionForce Attraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
-        for (Edge e : edges) {
-            Attraction.apply(e.getSource(), e.getTarget(), Math.pow(getWeight(e), getEdgeWeightInfluence()));
-        }
-
-        // Gravity
-        for (Node n : nodes) {
-            Repulsion.apply(n, getGravity() / getScalingRatio());
-        }
-
+        if(getEdgeWeightInfluence()==0){
+            for (Edge e : edges) {
+                Attraction.apply(e.getSource(), e.getTarget(), 1);
+            }
+        } else if(getEdgeWeightInfluence()==1){
+            for (Edge e : edges) {
+                Attraction.apply(e.getSource(), e.getTarget(), getWeight(e));
+            }
+        } else {
+            for (Edge e : edges) {
+                Attraction.apply(e.getSource(), e.getTarget(), Math.pow(getWeight(e), getEdgeWeightInfluence()));
+            }
+        }
+        
         // Auto adjust speed
         double totalSwinging = 0d;  // How much irregular movement
         double totalEffectiveTraction = 0d;  // Hom much useful movement
@@ -198,10 +221,10 @@
                     // when the node swings.
                     double swinging = Math.sqrt((nLayout.old_dx - nLayout.dx) * (nLayout.old_dx - nLayout.dx) + (nLayout.old_dy - nLayout.dy) * (nLayout.old_dy - nLayout.dy));
                     double factor = 0.1 * speed / (1f + speed * Math.sqrt(swinging));
-
+                    
                     double df = Math.sqrt(Math.pow(nLayout.dx, 2) + Math.pow(nLayout.dy, 2));
                     factor = Math.min(factor * df, 10.) / df;
-
+                    
                     double x = nData.x() + nLayout.dx * factor;
                     double y = nData.y() + nLayout.dy * factor;
 
@@ -220,7 +243,7 @@
                     double swinging = Math.sqrt((nLayout.old_dx - nLayout.dx) * (nLayout.old_dx - nLayout.dx) + (nLayout.old_dy - nLayout.dy) * (nLayout.old_dy - nLayout.dy));
                     //double factor = speed / (1f + Math.sqrt(speed * swinging));
                     double factor = speed / (1f + speed * Math.sqrt(swinging));
-
+                    
                     double x = nData.x() + nLayout.dx * factor;
                     double y = nData.y() + nLayout.dy * factor;
 
@@ -242,6 +265,7 @@
         for (Node n : graph.getNodes()) {
             n.getNodeData().setLayoutData(null);
         }
+        pool.shutdown();
         graph.readUnlockAll();
     }
 
@@ -251,6 +275,7 @@
         final String FORCEATLAS2_TUNING = NbBundle.getMessage(getClass(), "ForceAtlas2.tuning");
         final String FORCEATLAS2_BEHAVIOR = NbBundle.getMessage(getClass(), "ForceAtlas2.behavior");
         final String FORCEATLAS2_PERFORMANCE = NbBundle.getMessage(getClass(), "ForceAtlas2.performance");
+        final String FORCEATLAS2_THREADS = NbBundle.getMessage(getClass(), "ForceAtlas2.threads");
 
         try {
             properties.add(LayoutProperty.createProperty(
@@ -261,6 +286,13 @@
                     "getScalingRatio", "setScalingRatio"));
 
             properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.strongGravityMode.name"),
+                    FORCEATLAS2_TUNING,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.strongGravityMode.desc"),
+                    "isStrongGravityMode", "setStrongGravityMode"));
+
+            properties.add(LayoutProperty.createProperty(
                     this, Double.class,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.gravity.name"),
                     FORCEATLAS2_TUNING,
@@ -315,6 +347,13 @@
                     FORCEATLAS2_PERFORMANCE,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.barnesHutTheta.desc"),
                     "getBarnesHutTheta", "setBarnesHutTheta"));
+            
+            properties.add(LayoutProperty.createProperty(
+                    this, Integer.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.threads.name"),
+                    FORCEATLAS2_THREADS,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.threads.desc"),
+                    "getThreadsCount", "setThreadsCount"));
 
         } catch (Exception e) {
             e.printStackTrace();
@@ -337,6 +376,7 @@
         } else {
             setScalingRatio(10.0);
         }
+        setStrongGravityMode(false);
         setGravity(1.);
 
         // Behavior
@@ -359,6 +399,7 @@
             setBarnesHutOptimize(false);
         }
         setBarnesHutTheta(1.2);
+        setThreadsCount(2);
     }
 
     @Override
@@ -418,6 +459,14 @@
         this.scalingRatio = scalingRatio;
     }
 
+    public Boolean isStrongGravityMode() {
+        return strongGravityMode;
+    }
+
+    public void setStrongGravityMode(Boolean strongGravityMode) {
+        this.strongGravityMode = strongGravityMode;
+    }
+    
     public Double getGravity() {
         return gravity;
     }
@@ -425,6 +474,18 @@
     public void setGravity(Double gravity) {
         this.gravity = gravity;
     }
+    
+    public Integer getThreadsCount() {
+        return threadCount;
+    }
+
+    public void setThreadsCount(Integer threadCount) {
+        if(threadCount<1){
+            setThreadsCount(1);
+        } else {
+            this.threadCount = threadCount;
+        }
+    }
 
     public Boolean isOutboundAttractionDistribution() {
         return outboundAttractionDistribution;
 
=== modified file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/ForceFactory.java'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/ForceFactory.java	2011-06-05 21:30:01 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/ForceFactory.java	2011-08-30 14:28:25 +0000
@@ -22,6 +22,7 @@
 
 import org.gephi.graph.api.Node;
 import org.gephi.graph.api.NodeData;
+import org.openide.util.Exceptions;
 
 /**
  * Generates the forces on demand, here are all the formulas for attraction and repulsion.
@@ -43,6 +44,10 @@
             return new linRepulsion(coefficient);
         }
     }
+    
+    public RepulsionForce getStrongGravity(double coefficient){
+        return new strongGravity(coefficient);
+    }
 
     public AttractionForce buildAttraction(boolean logAttraction, boolean distributedAttraction, boolean adjustBySize, double coefficient) {
         if (adjustBySize) {
@@ -75,7 +80,7 @@
             }
         }
     }
-
+    
     public abstract class AttractionForce {
 
         public abstract void apply(Node n1, Node n2, double e); // Model for node-node attraction (e is for edge weight if needed)
@@ -141,7 +146,7 @@
 
                 nLayout.dx += xDist * factor;
                 nLayout.dy += yDist * factor;
-            }
+            }                
         }
 
         @Override
@@ -165,7 +170,7 @@
     }
 
     /*
-     * Repulsion force: Linear with Anti-collision
+     * Repulsion force: Strong Gravity (as a Repulsion Force because it is easier)
      */
     private class linRepulsion_antiCollision extends RepulsionForce {
 
@@ -252,6 +257,44 @@
         }
     }
 
+    private class strongGravity extends RepulsionForce {
+
+        private double coefficient;
+
+        public strongGravity(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2) {
+            // Not Relevant
+        }
+
+        @Override
+        public void apply(Node n, Region r) {
+            // Not Relevant
+        }
+
+        @Override
+        public void apply(Node n, double g) {
+            NodeData nData = n.getNodeData();
+            ForceAtlas2LayoutData nLayout = nData.getLayoutData();
+
+            // Get the distance
+            double xDist = nData.x();
+            double yDist = nData.y();
+            double distance = (float) Math.sqrt(xDist * xDist + yDist * yDist);
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = coefficient * nLayout.mass * g;
+
+                nLayout.dx -= xDist * factor;
+                nLayout.dy -= yDist * factor;
+            }
+        }
+    }
+
     /*
      * Attraction force: Linear
      */
 
=== added file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/NodesThread.java'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/NodesThread.java	1970-01-01 00:00:00 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/NodesThread.java	2011-08-30 14:28:25 +0000
@@ -0,0 +1,64 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.layout.plugin.forceAtlas2;
+
+import org.gephi.graph.api.Node;
+import org.gephi.layout.plugin.forceAtlas2.ForceFactory.RepulsionForce;
+
+/**
+ *
+ * @author Mathieu
+ */
+public class NodesThread implements Runnable{
+    private Node[] nodes;
+    private int from;
+    private int to;
+    private Region rootRegion;
+    private boolean barnesHutOptimize;
+    private RepulsionForce Repulsion;
+    private double barnesHutTheta;
+    private double gravity;
+    private RepulsionForce GravityForce;
+    private double scaling;
+    
+    public NodesThread(Node[] nodes, int from, int to, boolean barnesHutOptimize, double barnesHutTheta, double gravity, RepulsionForce GravityForce, double scaling, Region rootRegion, RepulsionForce Repulsion){
+        this.nodes = nodes;
+        this.from = from;
+        this.to = to;
+        this.rootRegion = rootRegion;
+        this.barnesHutOptimize = barnesHutOptimize;
+        this.Repulsion = Repulsion;
+        this.barnesHutTheta = barnesHutTheta;
+        this.gravity = gravity;
+        this.GravityForce = GravityForce;
+        this.scaling = scaling;
+    }
+    
+    @Override
+    public void run() {
+        // Repulsion
+        if (barnesHutOptimize) {
+            for (int nIndex = from; nIndex < to; nIndex++) {
+                Node n = nodes[nIndex];
+                rootRegion.applyForce(n, Repulsion, barnesHutTheta);
+            }
+        } else {
+            for (int n1Index = from; n1Index < to; n1Index++) {
+                Node n1 = nodes[n1Index];
+                for (int n2Index = 0; n2Index < n1Index; n2Index++) {
+                    Node n2 = nodes[n2Index];
+                    Repulsion.apply(n1, n2);
+                }
+            }
+        }
+
+        // Gravity
+        for (int nIndex = from; nIndex < to; nIndex++) {
+            Node n = nodes[nIndex];
+            GravityForce.apply(n, gravity / scaling);
+        }
+    }
+    
+}
 
=== added file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Operation.java'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Operation.java	1970-01-01 00:00:00 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Operation.java	2011-08-30 14:28:25 +0000
@@ -0,0 +1,13 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.layout.plugin.forceAtlas2;
+
+/**
+ *
+ * @author Mathieu
+ */
+public abstract class Operation {
+    public abstract void execute();   
+}
 
=== added file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeNodeAttract.java'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeNodeAttract.java	1970-01-01 00:00:00 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeNodeAttract.java	2011-08-30 14:28:25 +0000
@@ -0,0 +1,32 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.layout.plugin.forceAtlas2;
+
+import org.gephi.graph.api.Node;
+import org.gephi.layout.plugin.forceAtlas2.ForceFactory.AttractionForce;
+
+/**
+ *
+ * @author Mathieu
+ */
+public class OperationNodeNodeAttract extends Operation{
+    private Node n1;
+    private Node n2;
+    private AttractionForce f;
+    private double coefficient;
+    
+    public OperationNodeNodeAttract(Node n1, Node n2, AttractionForce f, double coefficient){
+        this.n1 = n1;
+        this.n2 = n2;
+        this.f = f;
+        this.coefficient = coefficient;
+    }
+    
+    @Override
+    public void execute() {
+        f.apply(n1, n2, coefficient);
+    }
+    
+}
 
=== added file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeNodeRepulse.java'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeNodeRepulse.java	1970-01-01 00:00:00 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeNodeRepulse.java	2011-08-30 14:28:25 +0000
@@ -0,0 +1,29 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.layout.plugin.forceAtlas2;
+
+import org.gephi.graph.api.Node;
+import org.gephi.layout.plugin.forceAtlas2.ForceFactory.RepulsionForce;
+
+/**
+ *
+ * @author Mathieu
+ */
+public class OperationNodeNodeRepulse extends Operation{
+    private Node n1;
+    private Node n2;
+    private RepulsionForce f;
+    
+    public OperationNodeNodeRepulse(Node n1, Node n2, RepulsionForce f){
+        this.n1 = n1;
+        this.n2 = n2;
+        this.f = f;
+    }
+    
+    @Override
+    public void execute() {
+        f.apply(n1, n2);
+    }
+}
 
=== added file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeRegionRepulse.java'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeRegionRepulse.java	1970-01-01 00:00:00 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeRegionRepulse.java	2011-08-30 14:28:25 +0000
@@ -0,0 +1,32 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.layout.plugin.forceAtlas2;
+
+import org.gephi.graph.api.Node;
+import org.gephi.layout.plugin.forceAtlas2.ForceFactory.RepulsionForce;
+
+/**
+ *
+ * @author Mathieu
+ */
+public class OperationNodeRegionRepulse extends Operation{
+    private Node n;
+    private Region r;
+    private RepulsionForce f;
+    private double theta;
+    
+    public OperationNodeRegionRepulse(Node n, Region r, RepulsionForce f, double theta){
+        this.n = n;
+        this.f = f;
+        this.r = r;
+        this.theta = theta;
+    }
+    
+    @Override
+    public void execute() {
+        r.applyForce(n, f, theta);
+    }
+    
+}
 
=== added file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeRepulse.java'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeRepulse.java	1970-01-01 00:00:00 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/OperationNodeRepulse.java	2011-08-30 14:28:25 +0000
@@ -0,0 +1,29 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.layout.plugin.forceAtlas2;
+
+import org.gephi.graph.api.Node;
+import org.gephi.layout.plugin.forceAtlas2.ForceFactory.RepulsionForce;
+
+/**
+ *
+ * @author Mathieu
+ */
+public class OperationNodeRepulse extends Operation{
+    private Node n;
+    private RepulsionForce f;
+    private double coefficient;
+    
+    public OperationNodeRepulse(Node n, RepulsionForce f, double coefficient){
+        this.n = n;
+        this.f = f;
+        this.coefficient = coefficient;
+    }
+    
+    @Override
+    public void execute() {
+        f.apply(n, coefficient);
+    }
+}
 
=== modified file 'LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Region.java'
--- LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Region.java	2011-06-05 21:30:01 +0000
+++ LayoutPlugin/src/org/gephi/layout/plugin/forceAtlas2/Region.java	2011-08-30 14:28:25 +0000
@@ -51,7 +51,7 @@
         updateMassAndGeometry();
     }
 
-    public void updateMassAndGeometry() {
+    private void updateMassAndGeometry() {
         if (nodes.size() > 1) {
             // Compute Mass
             mass = 0;
@@ -77,7 +77,7 @@
         }
     }
 
-    public void buildSubRegions() {
+    public synchronized void buildSubRegions() {
         if (nodes.size() > 1) {
             ArrayList<Node> leftNodes = new ArrayList<Node>();
             ArrayList<Node> rightNodes = new ArrayList<Node>();