Rename FishNutrient into NutrientRoutine

data/input/fishTryRealBV_CC.xml

@@ -10,7 +10,7 @@
 		<linfVonBert>60.0</linfVonBert>
 		<dMaxDisp>300.0</dMaxDisp>
 		<lFirstMaturity>40.0</lFirstMaturity>
-		<fishNutrient>
+		<nutrientRoutine>
 			<nutrientsOfInterest>
 				<string>N</string>
 				<string>P</string>
@@ -218,7 +218,7 @@
 					<double>0.02803</double>
 				</entry>
 			</compoJuvenile>
-		</fishNutrient>
+		</nutrientRoutine>
 
 		<fileNameInputForInitialObservation>data/input/reality/Obs1900.csv</fileNameInputForInitialObservation>
 		<centileForRange>0.95</centileForRange>

src/main/java/species/DiadromousFishGroup.java

@@ -62,7 +62,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 	 * Routine to compute nutrient fluxes operated by a single individual (TODO by a single super individual). 
 	 * 
 	 */
-	private  FishNutrient fishNutrient; 
+	private  NutrientRoutine nutrientRoutine; 
 	
 	public String fileNameInputForInitialObservation = "data/input/reality/Obs1900.csv";
 
@@ -265,7 +265,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 
 	
 		
-		diadromousFishGroup.fishNutrient = new FishNutrient(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning, 
+		diadromousFishGroup.nutrientRoutine = new NutrientRoutine(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning, 
 				aCompoCarcassPreSpawning, aCompoCarcassPostSpawning, aCompoGametes,
 				aJuvenileFeatures, aCompoJuveniles);
 		
@@ -507,9 +507,9 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 		return lFirstMaturity;
 	}
 
-	public  FishNutrient getFishNutrient() {
+	public  NutrientRoutine getNutrientRoutine() {
 		
-		return fishNutrient; 
+		return nutrientRoutine; 
 	}
 	
 	public void setlFirstMaturity(double lFirstMaturity) {

src/main/java/species/MigrateToSea.java

@@ -44,7 +44,7 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
 				List<DiadromousFish> fishes = basin.getFishs(group);
 				
 				// ON r-initialise notre map pour chauqe bassin 
-				for (String nutrient : group.getFishNutrient().getNutrientsOfInterest()) {
+				for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
 					totalOutputFluxes.put(nutrient, 0.); 
 				}
 				totalOutputFluxes.put("biomass", 0.); //cration de la biomasse 
@@ -54,10 +54,10 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
 						destination = group.getEnvironment().getAssociatedSeaBasin(fish.getPosition());
 						fishesToMove.add(new Duo<DiadromousFish, Basin>(fish, destination)); //Mentionne la sortie d'un poisson de la boucle 
 					
-						double biomass = group.getFishNutrient().getWeight(fish) * fish.getAmount(); 
+						double biomass = group.getNutrientRoutine().getWeight(fish) * fish.getAmount(); 
 						
 						if (fish.getStage()==Stage.IMMATURE) {
-							Map <String, Double> aFluxExportedByJuveniles= group.getFishNutrient().computeNutrientsExportForJuveniles(fish); 
+							Map <String, Double> aFluxExportedByJuveniles= group.getNutrientRoutine().computeNutrientsExportForJuveniles(fish); 
 							for (String nutrient: aFluxExportedByJuveniles.keySet()) {
 								totalOutputFluxes.put(nutrient,totalOutputFluxes.get(nutrient) + aFluxExportedByJuveniles.get(nutrient) * fish.getAmount()); 	
 							}

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

@@ -111,7 +111,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 
 					//Initiate the total fluxes for this basin 
 					Map<String, Double> totalInputFluxes = new Hashtable<String, Double>(); //On crer la Map pour stocker les flux 
-					for (String nutrient : group.getFishNutrient().getNutrientsOfInterest()) {
+					for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
 						totalInputFluxes.put(nutrient, 0.); // ON MET A JOUR NOTRE map 
 					}
 
@@ -193,10 +193,10 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 							if (survivalAmount > 0) {// SUperindividu est encore vivant mais il perd des effectifs 
 
 								//Export for fishes survived after spawning (survivalAmount) : excretion + gametes
-								Map <String, Double> aFluxAfterSurvival = group.getFishNutrient().computeNutrientsInputForSurvivalAfterSpawning(fish); 
+								Map <String, Double> aFluxAfterSurvival = group.getNutrientRoutine().computeNutrientsInputForSurvivalAfterSpawning(fish); 
 
 								//Export for fishes that dies after spawning (fish.getAmount - survivalAmount): excretion + gametes + carcasse 
-								Map<String, Double> aFluxForDeadFish = group.getFishNutrient().computeNutrientsInputForDeathAfterSpawning(fish); 
+								Map<String, Double> aFluxForDeadFish = group.getNutrientRoutine().computeNutrientsInputForDeathAfterSpawning(fish); 
 
 								for (String nutrient: aFluxAfterSurvival.keySet()) {
 									//For survival fish
@@ -207,7 +207,7 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 								}
 								
 								//compute biomass for dead fish 
-								biomass = group.getFishNutrient().getWeight(fish) * (fish.getAmount() - survivalAmount); 
+								biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount() - survivalAmount); 
 								totalInputFluxes.put("biomass", totalInputFluxes.get("biomass") + biomass);
 								
 								//update the amount of individual in the super-individual 
@@ -218,12 +218,12 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 								deadFish.add(fish);
 
 								//Export for fished died before spawning (fish.getAmount): carcasses + excretion + gametes 
-								Map<String, Double> aFlux = group.getFishNutrient().computeNutrientsInputForDeathAfterSpawning(fish); // 
+								Map<String, Double> aFlux = group.getNutrientRoutine().computeNutrientsInputForDeathAfterSpawning(fish); // 
 								
 								for (String nutrient: aFlux.keySet()) {
 									totalInputFluxes.put(nutrient,totalInputFluxes.get(nutrient) + aFlux.get(nutrient) * fish.getAmount()); //Fish.getAmount - survivalAmount = total fishes died. 
 								}
-								 biomass = group.getFishNutrient().getWeight(fish) * (fish.getAmount());
+								 biomass = group.getNutrientRoutine().getWeight(fish) * (fish.getAmount());
 								 totalInputFluxes.put("biomass", totalInputFluxes.get("biomass") + biomass); 
 							}
 						}