with optimized random draw

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

@@ -9,10 +9,12 @@ import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.ListIterator;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.TreeMap;
 
+import miscellaneous.BinomialForSuperIndividualGen;
 import miscellaneous.Duo;
 import miscellaneous.Miscellaneous;
 import miscellaneous.Trio;
@@ -29,6 +31,7 @@ import org.apache.commons.math3.optim.univariate.UnivariatePointValuePair;
 import org.openide.util.lookup.ServiceProvider;
 
 import umontreal.iro.lecuyer.probdist.NormalDist;
+import umontreal.iro.lecuyer.randvar.NormalACRGen;
 import umontreal.iro.lecuyer.randvar.NormalGen;
 
 import com.thoughtworks.xstream.XStream;
@@ -67,6 +70,13 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 	private boolean displayFluxesOnConsole = true;
 
 	private transient NormalGen genNormal;
+
+	/**
+	 * the random numbers generator for binomial draws
+	 * @unit --
+	 */
+	private transient BinomialForSuperIndividualGen aleaGen;
+
 	private transient MortalityFunction mortalityFunction;
 
 
@@ -86,8 +96,11 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 	@InitTransientParameters
 	public void initTransientParameters(Pilot pilot) {
 		super.initTransientParameters(pilot);
-		genNormal = new NormalGen( pilot.getRandomStream(),
+		genNormal = new NormalACRGen( pilot.getRandomStream(),
 				new NormalDist(0., 1.));
+
+		aleaGen = new BinomialForSuperIndividualGen(pilot.getRandomStream());
+
 		mortalityFunction=new MortalityFunction();
 		stockRecruitmentRelationship=  new StockRecruitmentRelationship();
 	}
@@ -104,7 +117,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 	public void doProcess(DiadromousFishGroup group) {
 		Time time = group.getEnvironment().getTime();
 		if (time.getSeason(group.getPilot()) == reproductionSeason){
-			List<DiadromousFish> deadFish = new ArrayList<DiadromousFish>();
+			//List<DiadromousFish> deadFish = new ArrayList<DiadromousFish>();
 			// a River
 			List<String> basinList = new ArrayList<String>() ;
 			basinList.add("Garonne");
@@ -164,6 +177,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 
 					// effective temperature for reproduction (priority to the ANG value) 
 					double tempEffectRep;
+					//CHECK if currentTemp can be removed
 					double currentTemp = riverBasin.getCurrentTemperature(group.getPilot());
 					if (Double.isNaN(group.getTempMinRep())){
 						tempEffectRep = Miscellaneous.temperatureEffect(riverBasin.getCurrentTemperature(group.getPilot()), tempMinRep, tempOptRep, tempMaxRep);
@@ -203,7 +217,11 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 					Map<Integer, Long> ageOfNativeSpawners = new TreeMap<Integer, Long>(); 
 
 					// compute the number of female spawners and keep the origine of the female spawners
-					for (DiadromousFish fish : fishInBasin){
+					ListIterator<DiadromousFish> fishIterator = fishInBasin.listIterator();
+					while (fishIterator.hasNext()) {
+						DiadromousFish fish = fishIterator.next();
+
+						//for (DiadromousFish fish : fishInBasin){
 
 						if (fish.isMature()) {
 
@@ -253,13 +271,12 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 
 							// survival after reproduction (semelparity or iteroparity) of SI (change the amount of the SI)
 							double biomass = 0.; 
-							survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction); 
-
+							survivalAmount = aleaGen.getSuccessNumber2(fish.getAmount(), survivalRateAfterReproduction); 
 
-							// update the amount of fish or kill the fish if survival amount = 0
-							// compute nutrient fluxes
+							// update the amount of fish or kill the fish if survival amount = 0		
 							if (survivalAmount > 0) {// SUperindividu est encore vivant mais il perd des effectifs 
 
+								// --------------------------------------------------------------------------------------- nutrient routine -----------------------------
 								//Export for one fish survived after spawning (survivalAmount) : excretion + gametes
 								Map <String, Double> aFluxAfterSurvival = group.getNutrientRoutine().computeNutrientsInputForSurvivalAfterSpawning(fish); 
 
@@ -287,14 +304,16 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 								//compute biomass for dead fish 
 								biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount() - survivalAmount); 
 								totalInputFluxes.get(spawnerOrigin).put("biomass", totalInputFluxes.get(spawnerOrigin).get("biomass") + biomass);
+								// --------------------------------------------------------------------------------------- nutrient routine -----------------------------
 
 								//update the amount of individual in the super-individual 
 								fish.setAmount(survivalAmount); 
 							}
 							else {
 								//Le superindividu est mort !!! 
-								deadFish.add(fish);
+								//deadFish.add(fish);
 
+								// --------------------------------------------------------------------------------------- nutrient routine -----------------------------
 								//Export for fished died after spawning (fish.getAmount): carcasses + excretion + gametes 
 								Map<String, Double> aFluxForDeadFish = group.getNutrientRoutine().computeNutrientsInputForDeathAfterSpawning(fish); // 
 
@@ -303,7 +322,11 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 									put(time.getYear(group.getPilot()), nutrient, fish.getBirthBasin().getName(), riverBasin.getName(), aFluxForDeadFish.get(nutrient) * (fish.getAmount() - survivalAmount));
 								}
 								biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount());
-								totalInputFluxes.get(spawnerOrigin).put("biomass", totalInputFluxes.get(spawnerOrigin).get("biomass") + biomass); 
+								totalInputFluxes.get(spawnerOrigin).put("biomass", totalInputFluxes.get(spawnerOrigin).get("biomass") + biomass);
+								// --------------------------------------------------------------------------------------- nutrient routine -----------------------------
+
+								// remove fish because fish is dead
+								fishIterator.remove();
 							}
 						}
 					}
@@ -368,7 +391,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 
 						// System.out.println("\t"+ riverBasin.getPopulationStatus());
 
-						String message;
+						/*String message;
 						if (Double.isNaN(riverBasin.getNativeSpawnerMortality()))
 							message="noSense";
 						else {
@@ -386,7 +409,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 								}
 							}
 						}
-						//System.out.println("\t"+message);
+						System.out.println("\t"+message);*/
 					}
 
 					// --------------------------------------------------------------------------------------------------
@@ -513,10 +536,10 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 					// --------------------------------------------------------------------------------------------------
 					// Remove deadfish and compute the related nutrient fluxes 
 					// --------------------------------------------------------------------------------------------------
-					for (DiadromousFish fish : deadFish){
+					/*	for (DiadromousFish fish : deadFish){
 						group.removeAquaNism(fish);
 					}
-					deadFish.clear();
+					deadFish.clear();*/
 
 					// -------------------------------------------------------
 					// display information