Activated the DemographicManager in BoidGraph.

It is actually created with a constant probability of 0.01 for birth and
death for each species.

A bug remains : a species disappear, is this tied to the display and
ui.class ??

src/org/graphstream/boids/Boid.java

@@ -109,6 +109,11 @@ public class Boid extends AdjacencyListNode {
 	}
 
 	public void checkNeighborhood(Boid... boids) {
+		if(getGraph().getNode(getId()) == null) {
+			System.err.printf("I do not exist any more !!!%n");
+			return;
+		}
+		
 		if (boids != null) {
 			Iterator<Boid> it = getNeighborNodeIterator();
 			LinkedList<Boid> toRemove = null;
@@ -141,8 +146,11 @@ public class Boid extends AdjacencyListNode {
 			}
 
 			for (Boid b2 : boids) {
-				if (getEdgeBetween(b2) == null)
-					getGraph().addEdge(getEdgeId(this, b2), this, b2);
+				if (getEdgeBetween(b2) == null) {
+					if(getGraph().getNode(b2.getId())!= null)
+					     getGraph().addEdge(getEdgeId(this, b2), this, b2);
+					else System.err.printf("%s does not exists !!%n", b2.getId());
+				}	
 			}
 		} else {
 			while (getDegree() > 0)

src/org/graphstream/boids/BoidGraph.java

@@ -135,9 +135,11 @@ public class BoidGraph extends AdjacencyListGraph {
 	 * Listeners for boid-graph specific events.
 	 */
 	protected ArrayList<BoidGraphListener> listeners = new ArrayList<BoidGraphListener>();
-
+	
 	/**
-	 * New context.
+	 * New boids simulation represented as an interaction graph.
+	 * 
+	 * <p>All parameters are set to defaults.</p>
 	 */
 	public BoidGraph() {
 		super("boids-context");
@@ -159,6 +161,14 @@ public class BoidGraph extends AdjacencyListGraph {
 		setForcesFactory(new NTreeForcesFactory(this));
 	}
 
+	/**
+	 * New boids simulation represented as an interaction graph.
+	 * 
+	 * <p>This pre-load a configuration from a DGS file.</p>
+	 * 
+	 * @param dgsConfig The initial configuration in DGS format.
+	 * @throws IOException If the DGS cannot be read.
+	 */
 	public BoidGraph(String dgsConfig) throws IOException {
 		this();
 		loadDGSConfiguration(dgsConfig);
@@ -207,6 +217,10 @@ public class BoidGraph extends AdjacencyListGraph {
 		config.removeSink(this);
 	}
 
+	/**
+	 * Set the factory used to instantiate the force system to use.
+	 * @param bff The force system factory.
+	 */
 	public void setForcesFactory(BoidForcesFactory bff) {
 		if (forcesFactory != null)
 			forcesFactory.end();
@@ -290,15 +304,19 @@ public class BoidGraph extends AdjacencyListGraph {
 		this.maxSteps = maxSteps;
 	}
 
+	/**
+	 * The random number generator used.
+	 * @return The random number generator.
+	 */
 	public Random getRandom() {
 		return random;
 	}
 
-	public BoidSpecies getOrCreateSpecies(String name) {
+	protected BoidSpecies getOrCreateSpecies(String name) {
 		return getOrCreateSpecies(name, null);
 	}
 
-	public BoidSpecies getOrCreateSpecies(String name, String clazz) {
+	protected BoidSpecies getOrCreateSpecies(String name, String clazz) {
 		BoidSpecies species = boidSpecies.get(name);
 
 		if (species == null) {
@@ -342,25 +360,54 @@ public class BoidGraph extends AdjacencyListGraph {
 		return species;
 	}
 
+	/**
+	 * The species with the given name.
+	 * @param name The species name.
+	 * @return The corresponding species or null if not found.
+	 */
 	public BoidSpecies getSpecies(String name) {
 		return boidSpecies.get(name);
 	}
 
+	/**
+	 * The number of boid species actually.
+	 * @return The number of boid species.
+	 */
 	public int getSpeciesCount() {
 		return boidSpecies.size();
 	}
 
+	/**
+	 * The species whose name is "default".
+	 * @return The default species.
+	 */
 	public BoidSpecies getDefaultSpecies() {
 		return getSpecies("default");
 	}
 
+	/**
+	 * Add a species with name "default" if does not yet exists.
+	 * @return The created default species or the old one if it was already present. 
+	 */
 	public BoidSpecies addDefaultSpecies() {
 		return getOrCreateSpecies("default");
 	}
 
+	/**
+	 * Remove a species.
+	 * 
+	 * This also removed all the boids of this species. You cannot remove the "default" species.
+	 * 
+	 * @param name The species name.
+	 */
 	public void deleteSpecies(String name) {
-		if (!name.equals("default"))
-			boidSpecies.remove(name);
+		if (!name.equals("default")) {
+			BoidSpecies species = boidSpecies.get(name);
+			if(species != null) {
+				species.release();
+				boidSpecies.remove(name);
+			}
+		}
 	}
 
 	// Commands
@@ -457,32 +504,32 @@ public class BoidGraph extends AdjacencyListGraph {
 		loop = true;
 
 		while (loop) {
-			stepBegins(step);
-
-			for (BoidSpecies sp : boidSpecies.values())
-				sp.terminateLoop();
-
-			sleep(sleepTime);
-
-			step++;
+			step();
 
 			if (maxSteps > 0 && step > maxSteps)
 				loop = false;
+
+			sleep(sleepTime);
 		}
 	}
 
 	public void step() {
-		stepBegins(step + 1);
-
-		for (BoidGraphListener listener : listeners) {
-			listener.step(step + 1);
-		}
+		step++;
+		stepBegins(step);
 	}
 
 	@Override
 	public void stepBegins(double step) {
-		super.stepBegins(step);
+		for (BoidSpecies sp : boidSpecies.values()) {
+			sp.terminateStep(step);
+		}
+		for (BoidGraphListener listener : listeners) {
+			listener.step(step);
+		}
+
 		forcesFactory.step();
+		
+		super.stepBegins(step);
 	}
 
 	public boolean isLooping() {
@@ -514,6 +561,17 @@ public class BoidGraph extends AdjacencyListGraph {
 	public void addBoidGraphListener(BoidGraphListener listener) {
 		listeners.add(listener);
 	}
+	
+	/**
+	 * Unregister a listener for boid specific events.
+	 * @param listener The listener to remove.
+	 */
+	public void removeBoidGraphListener(BoidGraphListener listener) {
+		int index = listeners.indexOf(listener);
+		if(index >= 0) {
+			listeners.remove(index);
+		}
+	}
 
 	@Override
 	protected void addNodeCallback(AbstractNode node) {

src/org/graphstream/boids/BoidGraphListener.java

@@ -44,7 +44,7 @@ public interface BoidGraphListener {
 	 * forces model.
 	 * @param time The current iteration time.
 	 */
-	void step(int time);
+	void step(double time);
 
 	/** 
 	 * One boid was added.

src/org/graphstream/boids/BoidSpecies.java

@@ -33,6 +33,7 @@ import java.util.HashMap;
 import java.util.Iterator;
 
 import org.graphstream.boids.BoidGraph;
+import org.graphstream.graph.Node;
 
 /**
  * Parameters for each boids species.
@@ -143,12 +144,17 @@ public class BoidSpecies implements Iterable<Boid> {
 	/**
 	 * Allow to create unique identifiers for boids.
 	 */
-	private int currentIndex = 0;
+	protected int currentIndex = 0;
 	
 	/**
 	 * Allow to create unique identifiers for boids.
 	 */
-	private long timestamp = System.nanoTime();
+	protected long timestamp = System.nanoTime();
+	
+	/**
+	 * Handle the addition or removal of boids.
+	 */
+	protected DemographicManager pop; 
 
 	/**
 	 * New default species with a random color.
@@ -177,6 +183,7 @@ public class BoidSpecies implements Iterable<Boid> {
 		inertia = 1.1f;
 		fearFactor = 1;
 		addSpeciesNameInUIClass = true;
+		pop = new DemographicManager.SpeciesDemographicManager(this, ctx, new Probability.ConstantProbability(0.01), new Probability.ConstantProbability(0.01));
 
 		this.color = new Color(ctx.random.nextFloat(), ctx.random.nextFloat(),
 				ctx.random.nextFloat());
@@ -325,10 +332,11 @@ public class BoidSpecies implements Iterable<Boid> {
 	/**
 	 * This method is called by {@link org.graphstream.boids.BoidGraph} at the
 	 * end of each step. It can be used by sub-classes to add some code.
+     * @param time The current boid graph time.
 	 */
-	public void terminateLoop() {
-		// Do nothing.
-		// Can be used by extending classes.
+	public void terminateStep(double time) {
+System.err.printf("## pop for %s%n", getName());
+		pop.step(time);
 	}
 
 	/**
@@ -568,7 +576,41 @@ public class BoidSpecies implements Iterable<Boid> {
 	public void setAngleOfView(double aov) {
 		angleOfView = aov;
 	}
-
+	
+	/**
+	 * The probability that a boids clones itself.
+	 * @param probability A probability instance.
+	 */
+	public void setReproductionProbability(Probability probability) {
+		pop.setReproduceCondition(probability);
+	}
+	
+	/**
+	 * The probability that a boids die.
+	 * @param probability A probability instance.
+	 */
+	public void setDeathCondition(Probability probability) {
+		pop.setDeathProbability(probability);
+	}
+	
+	/**
+	 * Unregister this species from the boids graph.
+	 * 
+	 * This removes all boids pertaining to this species, and release the link with the graph.
+	 */
+	public void release() {
+		pop.release();
+		
+		Iterator<Node> i = ctx.getNodeIterator();
+		
+		while(i.hasNext()) {
+			Boid b = (Boid) i.next();
+			if(b.getSpecies() == this) {
+				i.remove();
+			}
+		}
+	}
+	
 	/*
 	 * (non-Javadoc)
 	 * 

src/org/graphstream/boids/DemographicManager.java

@@ -154,7 +154,7 @@ public class DemographicManager implements BoidGraphListener {
 			b = futureParents.poll();
 			
 			String id = b.getSpecies().createNewId();
-			
+System.err.printf("  -> adding boid %s%n", id);
 			ctx.addNode(id);
 //			ctx.addBoid(b.getSpecies(), b.getPosition().x, b.getPosition().y, b
 //					.getPosition().z);
@@ -181,6 +181,8 @@ public class DemographicManager implements BoidGraphListener {
 			}
 		}
 
+System.err.printf("Preparing to remove %d boids and add %d boids.%n", toRemove.size(), futureParents.size());
+		
 		makeLove();
 		killAll();
 
@@ -199,9 +201,16 @@ public class DemographicManager implements BoidGraphListener {
 	 * Call this method after each step of boid computation, to add or remove boids according to
 	 * reproduction rules. 
 	 */
-	public void step(int time) {
+	public void step(double time) {
 		check();
 	}
+	
+	/**
+	 * Release this manager, and remove as a listener for the graph.
+	 */
+	public void release() {
+		ctx.removeBoidGraphListener(this);
+	}
 
 	/**
 	 * A demographic manager that handles boids species.

src/org/graphstream/boids/forces/ntree/NTreeForces.java

@@ -65,6 +65,7 @@ public class NTreeForces extends BoidForces {
 	 * 
 	 * @see org.graphstream.boids.BoidForces#getPosition()
 	 */
+	@Override
 	public Point3 getPosition() {
 		return p.getPosition();
 	}
@@ -74,6 +75,7 @@ public class NTreeForces extends BoidForces {
 	 * 
 	 * @see org.graphstream.boids.BoidForces#setPosition(double, double, double)
 	 */
+	@Override
 	public void setPosition(double x, double y, double z) {
 		p.setPosition(x, y, z);
 	}
@@ -83,6 +85,7 @@ public class NTreeForces extends BoidForces {
 	 * 
 	 * @see org.graphstream.boids.BoidForces#getNextPosition()
 	 */
+	@Override
 	public Point3 getNextPosition() {
 		return p.getNextPosition();
 	}
@@ -91,10 +94,10 @@ public class NTreeForces extends BoidForces {
 	 * Recursively explore the n-tree to search for intersection cells, and the
 	 * visible boids.
 	 * 
-	 * @param source
-	 *            The boid the forces are computed on.
 	 * @param cell
 	 *            The cell to explore recursively.
+	 * @param contacts
+	 *            The set of visible boids to build by exploration.
 	 */
 	protected void exploreTree(Cell cell, Set<Boid> contacts) {
 		if (intersection(boid, cell)) {
@@ -113,10 +116,10 @@ public class NTreeForces extends BoidForces {
 	 * A leaf cell has been found that is in intersection with the boid area,
 	 * computes the forces from this cell.
 	 * 
-	 * @param source
-	 *            The boid the forces are computed on.
 	 * @param cell
 	 *            The cell.
+	 * @param contacts
+	 *            The set of visible boids to build by exploration.
 	 */
 	protected void forcesFromCell(Cell cell, Set<Boid> contacts) {
 		Iterator<? extends Particle> particles = cell.getParticles();
@@ -190,6 +193,7 @@ public class NTreeForces extends BoidForces {
 	 * 
 	 * @see org.graphstream.boids.BoidForces#getNeighborhood()
 	 */
+	@Override
 	public Collection<Boid> getNeighborhood() {
 		HashSet<Boid> neigh = new HashSet<Boid>();
 		Cell startCell = p.getCell().getTree().getRootCell();

src/org/graphstream/boids/forces/ntree/NTreeForcesFactory.java

@@ -166,7 +166,7 @@ public class NTreeForcesFactory implements BoidForcesFactory, ElementSink {
 	 */
 	public void nodeRemoved(String sourceId, long timeId, String nodeId) {
 		Boid b = ctx.getNode(nodeId);
-		pbox.removeParticle(((NTreeForces) b.getForces()).p);
+		pbox.removeParticle(((NTreeForces) b.getForces()).p.getId());
 	}
 
 	/*