remoce basinDistancesPerBasin frpm DisperseAndMigrateToRiverBasic

the information is assessible through  getNeighboursDistances()

src/main/java/species/DisperseAndMigrateToRiver.java

 package species;
 
 import java.util.ArrayList;
-import java.util.TreeMap;
 import java.util.List;
 import java.util.Map;
+import java.util.TreeMap;
+
+import org.openide.util.lookup.ServiceProvider;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
 
 import environment.Basin;
 import environment.BasinNetwork;
-import environment.RiverBasin;
-import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import miscellaneous.BinomialForSuperIndividualGen;
-import miscellaneous.Miscellaneous;
-
-import org.openide.util.lookup.ServiceProvider;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
 
 @ServiceProvider(service = AquaNismsGroupProcess.class)
 public class DisperseAndMigrateToRiver extends DisperseAndMigrateToRiverBasic {
 
-	private double pHoming=0.5;
+	private double pHoming = 0.5;
 	private Season riverMigrationSeason = Season.SPRING;
 	private double alpha2Rep = 0.;
 
 
-
 	public static void main(String[] args) {
-		System.out.println((new XStream(new DomDriver()))
-				.toXML(new DisperseAndMigrateToRiver()));
+		System.out.println((new XStream(new DomDriver())).toXML(new DisperseAndMigrateToRiver()));
 	}
-//TODO need to be corrected to remove fish remove
+
+
+	// TODO need to be corrected to remove fish remove
 	@Override
 	public void doProcess(DiadromousFishGroup group) {
-		
-		if (group.getEnvironment().getTime().getSeason(group.getPilot()) == riverMigrationSeason ){
+
+		if (group.getEnvironment().getTime().getSeason(group.getPilot()) == riverMigrationSeason) {
 			BasinNetwork bn = group.getEnvironment();
 			double dMaxDispFish = 0.;
 
 			long amountWithHoming, strayedAmount;
 
-			Map<RiverBasin, Double> distBasOfFish;
+			Map<Basin, Double> distBasOfFish;
 
 			List<DiadromousFish> deadFish = new ArrayList<DiadromousFish>();
 			List<DiadromousFish> newFish = new ArrayList<DiadromousFish>();
 
-			for (DiadromousFish fish : group.getAquaNismsList() ) {
-		
-				if (fish.isMature())   {
+			for (DiadromousFish fish : group.getAquaNismsList()) {
+
+				if (fish.isMature()) {
 					// fish with homing
-					amountWithHoming = BinomialForSuperIndividualGen.getSuccessNumber(group.getPilot(), fish.getAmount(), pHoming); // seuil par d�faut fix� � 50								
+					amountWithHoming = BinomialForSuperIndividualGen.getSuccessNumber(group.getPilot(), fish.getAmount(),
+							pHoming); // seuil par d�faut fix� � 50
+
+					// strayed fish
+					strayedAmount = fish.getAmount() - amountWithHoming;
 
-					// strayed fish 
-					strayedAmount = fish.getAmount() - amountWithHoming;					
-					
 					if (strayedAmount != 0) {
 						// On r�cup�re les info du poids des bassin par rapport � la position du poisson
-						Map<Basin,Double> accBasOfFish= new TreeMap<Basin, Double>(basinWeightsPerBasin.get(fish.getPosition()));
-						//accBasOfFish = accessibleBasinsPerBasin.get(fish.getPosition());						
+						Map<Basin, Double> accBasOfFish = new TreeMap<Basin, Double>(
+								basinWeightsPerBasin.get(fish.getPosition()));
+						// accBasOfFish = accessibleBasinsPerBasin.get(fish.getPosition());
 
 						// On retire certains bassins si on consid�re une distance max de dispersion
-						distBasOfFish = basinDistancesPerBasin.get(fish.getPosition());
-						if (group.getdMaxDisp() != 0){
+						distBasOfFish = fish.getPosition().getNeighboursDistances();
+						if (group.getdMaxDisp() != 0) {
 							// TODO pourquoi distbasoffish peut �tre nul ?
-							if (distBasOfFish != null){
-								dMaxDispFish = (group.getdMaxDisp()/group.getLinfVonBert(fish))*fish.getLength();
+							if (distBasOfFish != null) {
+								dMaxDispFish = (group.getdMaxDisp() / group.getLinfVonBert(fish)) * fish.getLength();
 								// load accessible basins
-								for (Basin surroundingBasin : distBasOfFish.keySet()){
+								for (Basin surroundingBasin : distBasOfFish.keySet()) {
 									Double distance = distBasOfFish.get(surroundingBasin);
-									//System.out.println("pour le poisson " + fish.hashCode() + " situ� dans le bassin " + basin.getName() + " et n� dans le bassin " + fish.getBirthBasin().getName());
-									//System.out.println("la distance vaut " + distance + " pour le bassin " + surroundingBasin.getName());
+									// System.out.println("pour le poisson " + fish.hashCode() + " situ� dans le bassin
+									// " + basin.getName() + " et n� dans le bassin " + fish.getBirthBasin().getName());
+									// System.out.println("la distance vaut " + distance + " pour le bassin " +
+									// surroundingBasin.getName());
 									if (distance >= dMaxDispFish) {
 										accBasOfFish.remove(surroundingBasin);
 									}
 								}
-							}							
+							}
 						}
 
 						// We fill the weight table
 						double totalWeight = 0.;
 						double probToGo = 0.;
 						long amountToGo = 0;
-						// TODO Qu'est ce qui se passe si AccBasOfFish est vide... �a beug pas mais c'est pas tr�s clair... donc � v�rifier
-						for (Basin accBasin : accBasOfFish.keySet()){
+						// TODO Qu'est ce qui se passe si AccBasOfFish est vide... �a beug pas mais c'est pas tr�s
+						// clair... donc � v�rifier
+						for (Basin accBasin : accBasOfFish.keySet()) {
 							double accBasinWeightLogit = accBasOfFish.get(accBasin) + alpha2Rep * fish.getLength();
-							double accBasinWeight = 1 / (1 + Math.exp(- accBasinWeightLogit));
+							double accBasinWeight = 1 / (1 + Math.exp(-accBasinWeightLogit));
 							accBasOfFish.put(accBasin, accBasinWeight);
 							totalWeight += accBasinWeight;
 						}
 
-						// compute sequentially the prob to go into a  basin
-						for (Basin accBasin : accBasOfFish.keySet()){
+						// compute sequentially the prob to go into a basin
+						for (Basin accBasin : accBasOfFish.keySet()) {
 							probToGo = accBasOfFish.get(accBasin) / totalWeight;
-							amountToGo = BinomialForSuperIndividualGen.getSuccessNumber(group.getPilot(), strayedAmount, probToGo);
+							amountToGo = BinomialForSuperIndividualGen.getSuccessNumber(group.getPilot(), strayedAmount,
+									probToGo);
 
-							if (amountToGo > 0){
-								newFish.add(fish.duplicateWithNewPositionAndAmount(group.getPilot(), bn.getAssociatedRiverBasin(accBasin), amountToGo));			
+							if (amountToGo > 0) {
+								newFish.add(fish.duplicateWithNewPositionAndAmount(group.getPilot(),
+										bn.getAssociatedRiverBasin(accBasin), amountToGo));
 							}
 
 							totalWeight -= accBasOfFish.get(accBasin);
-							strayedAmount -= amountToGo;	
+							strayedAmount -= amountToGo;
 						}
 					}
 
 					// update fish with homing
-					if (amountWithHoming > 0){
+					if (amountWithHoming > 0) {
 						fish.setAmount(amountWithHoming);
-						// retour soit dans le bassin de naissance pour les semelpares 
+						// retour soit dans le bassin de naissance pour les semelpares
 						// soit dans le dernier bassin de reproduction pour les it�ropares
 						fish.moveTo(group.getPilot(), bn.getAssociatedRiverBasin(fish.getPosition()), group);
 					} else {
@@ -116,11 +120,11 @@ public class DisperseAndMigrateToRiver extends DisperseAndMigrateToRiverBasic {
 					}
 				}
 			}
-			
-			for (DiadromousFish fish : deadFish){
+
+			for (DiadromousFish fish : deadFish) {
 				group.removeAquaNism(fish);
 			}
-			for (DiadromousFish fish : newFish){
+			for (DiadromousFish fish : newFish) {
 				group.addAquaNism(fish);
 			}
 		}

src/main/java/species/DisperseAndMigrateToRiverBasic.java

@@ -86,40 +86,41 @@ public class DisperseAndMigrateToRiverBasic extends AquaNismsGroupProcess<Diadro
 	 */
 	protected transient Map<SeaBasin, Map<RiverBasin, Double>> basinWeightsPerBasin;
 
+
 	/**
 	 * a map associtaing a sea bassin with the distance for each river bassin <key> SeaBasin <value> <key> RiverBasin
 	 * <value> distance between the river Basin and the river basin associated with the sea basin
 	 */
-	@Deprecated
-	protected transient Map<SeaBasin, Map<RiverBasin, Double>> basinDistancesPerBasin;
-
+	// @Deprecated
+	// protected transient Map<SeaBasin, Map<RiverBasin, Double>> basinDistancesPerBasin;
 
 	@Override
 	@InitTransientParameters
 	public void initTransientParameters(Pilot pilot) {
 		super.initTransientParameters(pilot);
-		// calcul les poids des bassins voisins qui ne d�pendent pas des poissons pour chaque SeaBassin
+
 		BasinNetwork bn = (BasinNetwork) pilot.getAquaticWorld().getEnvironment();
-		basinDistancesPerBasin = new TreeMap<SeaBasin, Map<RiverBasin, Double>>();
+
+		// calcul les poids des bassins voisins qui ne d�pendent pas des poissons pour chaque SeaBassin
 		basinWeightsPerBasin = new TreeMap<SeaBasin, Map<RiverBasin, Double>>();
 
+		// Compute the weight of each river basin
 		for (SeaBasin seaBas : bn.getSeaBasins()) {
-			// compute the distance with between seaBas and all the river basins
-			Map<RiverBasin, Double> mapDist = new TreeMap<RiverBasin, Double>();
-			// Compute the weight of each river basin
+
 			Map<RiverBasin, Double> mapWeight = new TreeMap<RiverBasin, Double>();
+			RiverBasin associatedRiverBasin;
 
-			for (Entry<Basin, Double> entry : bn.getNeighboursWithDistance(seaBas).entrySet()) {
-				RiverBasin associatedRiverBasin = (RiverBasin) bn.getAssociatedRiverBasin(entry.getKey());
-				mapDist.put(associatedRiverBasin, entry.getValue());
+			for (Entry<Basin, Double> entry : seaBas.getNeighboursDistances().entrySet()) {
+				associatedRiverBasin = (environment.RiverBasin) entry.getKey();
+				// RiverBasin associatedRiverBasin = (RiverBasin) bn.getAssociatedRiverBasin(entry.getKey());
 
 				double weight = alpha0Rep - alpha1Rep * ((entry.getValue() - meanInterDistance) / standardDeviationInterDistance)
 						+ alpha3Rep
 								* ((associatedRiverBasin.getAttractiveSurface() - meanBvSurface) / standardDeviationBvSurface);
+
 				mapWeight.put(associatedRiverBasin, weight);
 
 			}
-			basinDistancesPerBasin.put(seaBas, mapDist);
 			basinWeightsPerBasin.put(seaBas, mapWeight);
 		}
 	}