Remove Duo

src/main/java/species/DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin.java

@@ -5,6 +5,7 @@ import java.util.List;
 import java.util.ListIterator;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.TreeMap;
 
 import environment.Basin;
 import environment.BasinNetwork;
@@ -28,61 +29,61 @@ import miscellaneous.Duo;
 @ServiceProvider(service = AquaNismsGroupProcess.class)
 public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends DisperseAndMigrateToRiverBasic {
 
-	
+
 	/**
 	 * the season when fish migrate to the river to reproduce
 	 * @unit
 	 */
 	private Season riverMigrationSeason = Season.SPRING;
-	
+
 	/**
 	 *  the homing  probalilty during the installation of new populations ( to reach kind of equilibrium)
 	 * @unit
 	 */
 	private double pHomingForReachEquil = 1.0;
-	
+
 	/**
 	 *  the homing  probalilty after the installation of new populations ( after reaching an equilibrium)
 	 * @unit
 	 */
 	private double pHomingAfterEquil = 0.8;
-	
+
 	/**
 	 * Number of year for newly created populations to be installed ( to reach an equilibrium)
 	 * @unit
 	 */
 	private long NbYearForInstallPop = 50;
 
-	
+
 	/** the coefficient associated with  the fish size in the logistic function used to calculate the probability to disperse
 	 * @unit -
 	 */
 	private double alpha2Rep = 0.;
-	
+
 	/** 
 	 * the mean length used to standardize the fish length in the logistic function that calculates the probability to disperse
 	 * @unit -
 	 */
 	private double meanSpawnersLengthAtRepro = 45.;
-	
+
 	/** 
 	 * the length standard deviation  used to standardize the fish length in the logistic function that calculates the probability to disperse
 	 * @unit -
 	 */
 	private double standardDeviationOfSpawnersLengthAtRepro = 2.; // for standard core values...
-	
+
 	/**
 	 * the weigth of the death bassin ( for strayers that do not find a catcment) used to calculate the probability to disperse
 	 * @unit
 	 */
 	private double weightOfDeathBasin = 0.2;
-	
+
 	/**
 	 *  a bollean to kill of the strayers (used to determine if a catchment is a souce or a sink) the year given by yearOfTheKilling
 	 * @unit
 	 */
 	private boolean killStrayers;
-	
+
 	/**
 	 * the year when the strayers are killed (used to determine if a catchment is a souce or a sink) if killStrayers is true
 	 * @unit
@@ -115,14 +116,13 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
 			//List<DiadromousFish> newFish = new ArrayList<DiadromousFish>();
 
 			// creation of the death basin (for the lost strayers)
-			//TODO move as a transient field
-			Basin deathBasin = new Basin(-1, "deathBasin", 0, 0, 0, 0);
-			
+			//Basin deathBasin = new Basin(-1, "deathBasin", 0, 0, 0, 0);
+
 			//List<Duo<DiadromousFish, Basin>> fishesToMove = new ArrayList<Duo<DiadromousFish, Basin>>();
 			for (SeaBasin departure : group.getEnvironment().getSeaBasins()) {
-				
+
 				RiverBasin homingDestination = (RiverBasin) bn.getAssociatedRiverBasin(departure);
-				
+
 				List<DiadromousFish> fishes = departure.getFishs(group);
 				if (fishes != null) {
 					//for (DiadromousFish fish : fishes) {
@@ -131,7 +131,7 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
 						DiadromousFish fish=fishIterator.next();
 						// verify that fish is in a sea basin
 						//assert fish.getPosition().getType() == Basin.TypeBassin.SEA;
-						
+
 						if (fish.isMature()) {
 							// fish with homing
 							amountWithHoming = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), pHoming); // seuil par d�faut fix� � 50								
@@ -156,17 +156,18 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
 									accBasOfFish.add(duo);
 								}
 
+
 								// We fill the weight table
 								double totalWeight = 0.;
 								double probToGo = 0.;
 								long amountToGo = 0;
-								// TODO manage the case when AccBasOfFish is empty
+								/*// TODO manage the case when AccBasOfFish is empty
 								for (Duo<Basin, Double> accBasin : accBasOfFish) {
 									// total weight for the basin
 									Basin b = accBasin.getFirst();
 									Double weight = accBasin.getSecond();
 									double accBasinWeight = 1 / (1 + Math.exp(-(weight + weightFishLength)));
-									
+
 									// put weight to 0 for unused basins
 									if (group.isThereBasinToUpdate()){
 										if (time.getYear(group.getPilot()) >= group.getYearOfTheUpdate()
@@ -177,28 +178,40 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
 									}
 									accBasin.setSecond(accBasinWeight);
 									totalWeight += accBasinWeight;
+								}*/
+
+								Map<RiverBasin, Double> basinWeightsFromDeparture = new TreeMap<RiverBasin, Double>();
+								for (Entry<RiverBasin, Double> entry : basinWeightsPerBasin.get(departure).entrySet()) {	
+									double accBasinWeight = 1. / (1. + Math.exp(-(entry.getValue() + weightFishLength)));
+									
+									// put weight to 0 for unused basins
+									if (group.isThereBasinToUpdate()){
+										if (time.getYear(group.getPilot()) >= group.getYearOfTheUpdate()
+												&& group.getPattractive(entry.getKey().getName()) == 0){
+											//TODO use correctely getPaccessible
+											accBasinWeight = 0 ;
+										}
+									}
+									totalWeight += accBasinWeight;
+									basinWeightsFromDeparture.put (entry.getKey(),accBasinWeight );
 								}
 
-								// add the deathBasin in the list
+								// sum the deathBasin weight in the list
 								//accBasOfFish.add(new Duo<Basin, Double>(deathBasin, weightOfDeathBasin));
 								totalWeight = totalWeight + weightOfDeathBasin;
 
 								// compute sequentially the prob to go into a  basin
-								for (Duo<Basin, Double> accBasin : accBasOfFish) {
-									Basin b = accBasin.getFirst();
-									Double weight = accBasin.getSecond();
+								for (Entry<RiverBasin, Double> entry : basinWeightsPerBasin.get(departure).entrySet()) {	
+									RiverBasin strayerDestination = entry.getKey();
+									Double weight = entry.getValue();
 									probToGo = weight / totalWeight;
 									amountToGo = Miscellaneous.binomialForSuperIndividual(group.getPilot(), strayedAmount, probToGo);
 
 									if (amountToGo > 0) {
-										if (b.getId() != -1) {
-											RiverBasin  strayerDestination = (RiverBasin) bn.getAssociatedRiverBasin(b);
+				
+											//RiverBasin  strayerDestination = (RiverBasin) bn.getAssociatedRiverBasin(b);
 											strayerDestination.addFish(fish.duplicateWithNewPositionAndAmount(group.getPilot(), strayerDestination, amountToGo), group);
-										}
-										//else{
-											//TODO add to the cemetery 
-											//deadFish.add(fish.duplicateWithNewPositionAndAmount(accBasin, amountToGo));
-											//}
+
 									}
 									totalWeight -= weight;
 									strayedAmount -= amountToGo;
@@ -220,7 +233,7 @@ public class DisperseAndMigrateToRiverWithMultiNomDistriAndDeathBasin extends Di
 							/*else {
 								deadFish.add(fish);
 							}*/
-							
+
 							fishIterator.remove();
 						}
 					}