with writing of fluxes

data/input/fishTryRealBV_CC.xml

@@ -227,6 +227,7 @@
 		<yearOfTheUpdate>0</yearOfTheUpdate>
 		<basinsToUpdateFile>data/input/reality/basinsToUpdate.csv</basinsToUpdateFile>
 		<outputPath>data/output/</outputPath>
+		<fileNameFluxes>nutrientFluxes</fileNameFluxes>
 		<processes>
 			<processesAtBegin>
 				<species.PopulateBasinNetworkWithANorthLimit>
@@ -306,11 +307,13 @@
 					<maxNumberOfSuperIndividualPerReproduction>50.0
 					</maxNumberOfSuperIndividualPerReproduction>
 					<withDiagnose>false</withDiagnose>
+					<displayFluxesOnConsole>false</displayFluxesOnConsole>
 				</species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 
 				<species.MigrateToSea>
 					<seaMigrationSeason>SUMMER</seaMigrationSeason>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<displayFluxesOnConsole>false</displayFluxesOnConsole>
 				</species.MigrateToSea>
 
 				<environment.updateTemperatureInRealBasin>

src/main/java/species/DiadromousFishGroup.java

@@ -13,7 +13,10 @@ import fr.cemagref.simaqualife.kernel.Processes;
 import fr.cemagref.simaqualife.pilot.Pilot;
 
 import java.awt.Color;
+import java.io.BufferedWriter;
+import java.io.File;
 import java.io.FileReader;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
@@ -65,7 +68,7 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 	private  NutrientRoutine nutrientRoutine; 
 	
 	public String fileNameInputForInitialObservation = "data/input/reality/Obs1900.csv";
-
+	
 	/**
 	 *  centile to calucale the range of species distribution
 	 * @unit
@@ -100,6 +103,11 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 	private String basinsToUpdateFile = "data/input/reality/basinsToUpdate.csv";
 
 	private String outputPath = "data/output/";
+	
+	private String fileNameFluxes = "fluxes";
+	
+	private transient BufferedWriter bWForFluxes;
+	private transient String sep;
 
 	/**
 	 *  map
@@ -394,6 +402,35 @@ public class DiadromousFishGroup extends AquaNismsGroup< DiadromousFish, BasinNe
 			kOpt = parameterSets.get(parameterSetLine-1).getFirst();
 			tempMinRep = parameterSets.get(parameterSetLine-1).getSecond();
 		}
+		
+		// open an bufferad writer to export fluxes
+		if (fileNameFluxes != null){
+			sep = ";";
+		    new File(this.outputPath +fileNameFluxes).getParentFile().mkdirs();
+			try {
+				bWForFluxes = new BufferedWriter(new FileWriter(new File(this.outputPath+
+						fileNameFluxes +this.getSimulationId()+ ".csv")));
+
+				bWForFluxes.write("timestep"+sep+"year"+sep+"season"+sep+"basin"
+						+sep+"fluxType"+sep+"origine"+sep+"biomass");
+				for (String nutrient : nutrientRoutine.getNutrientsOfInterest()) {
+					bWForFluxes.write(sep+nutrient);
+				}
+				bWForFluxes.write("\n");
+
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}
+	}
+
+	
+	
+	/**
+	 * @return the bWForFluxes
+	 */
+	public BufferedWriter getbWForFluxes() {
+		return bWForFluxes;
 	}
 
 	public double getKOpt(){

src/main/java/species/MigrateToSea.java

@@ -8,6 +8,9 @@ import environment.RiverBasin;
 import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
@@ -15,7 +18,6 @@ import java.util.Map;
 
 import miscellaneous.Duo;
 import species.DiadromousFish.Stage;
-
 import org.openide.util.lookup.ServiceProvider;
 
 @ServiceProvider(service = AquaNismsGroupProcess.class)
@@ -23,6 +25,8 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
 
 	private Season seaMigrationSeason = Season.SUMMER;	
 
+	private boolean displayFluxesOnConsole = true;
+
 	public static void main(String[] args) {
 		System.out.println((new XStream(new DomDriver()))
 				.toXML(new MigrateToSea()));
@@ -33,48 +37,65 @@ public class MigrateToSea extends AquaNismsGroupProcess<DiadromousFish, Diadromo
 
 		if (Time.getSeason(group.getPilot()) == seaMigrationSeason ){
 			Basin destination;
-			
-			//On crer la Map pour stocker les flux d'export
+
+			//On cr�er la Map pour stocker les flux d'export
 			Map<String, Double> totalOutputFluxes = new Hashtable<String, Double>(); 
-			
+
 			List<Duo<DiadromousFish,Basin>> fishesToMove = new ArrayList<Duo<DiadromousFish,Basin>>();
 			for (int i = 0; i < group.getEnvironment().getRiverBasins().length; i++) {
 				RiverBasin basin = group.getEnvironment().getRiverBasins()[i];
 				//Fish move to sea and compute the related export of nutrients 
 				List<DiadromousFish> fishes = basin.getFishs(group);
-				
-				// ON r-initialise notre map pour chauqe bassin 
+
+				// ON r�-initialise notre map pour chauqe bassin 
 				for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
 					totalOutputFluxes.put(nutrient, 0.); 
 				}
-				totalOutputFluxes.put("biomass", 0.); //cration de la biomasse 
-				
+				totalOutputFluxes.put("biomass", 0.); //cr�ation de la biomasse 
+
 				if (fishes!=null) {
 					for (DiadromousFish fish : fishes) {
 						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.getNutrientRoutine().getWeight(fish) * fish.getAmount(); 
-						
+
 						if (fish.getStage()==Stage.IMMATURE) {
 							Map <String, Double> aFluxExportedByJuveniles= group.getNutrientRoutine().computeNutrientsExportForJuveniles(fish); 
 							for (String nutrient: aFluxExportedByJuveniles.keySet()) {
 								totalOutputFluxes.put(nutrient,totalOutputFluxes.get(nutrient) + aFluxExportedByJuveniles.get(nutrient) * fish.getAmount()); 	
 							}
-							
+
 							totalOutputFluxes.put("biomass", totalOutputFluxes.get("biomass") + biomass); 
 						}
 					}     
 				}
-				
+
 				for (Duo<DiadromousFish,Basin> duo : fishesToMove) {
-					duo.getFirst().moveTo(group.getPilot(), duo.getSecond(), group); //on dplace les poissons dans le fichier MoveTo et on dnote la destination du poisson.
+					duo.getFirst().moveTo(group.getPilot(), duo.getSecond(), group); //on d�place les poissons dans le fichier MoveTo et on d�note la destination du poisson.
+				}
+
+				if (displayFluxesOnConsole)
+					System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";EXPORT;"
+							+ basin.getName() + "; " + totalOutputFluxes);
+
+				BufferedWriter bW = group.getbWForFluxes();
+				if ( bW != null) {
+					try {
+
+						bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) 
+						+";"+ basin.getName() +  ";IMPORT; NONE");
+						bW.write(";" + totalOutputFluxes.get("biomass"));
+						for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+							bW.write(";" + totalOutputFluxes.get(nutrient));
+						}
+						bW.write("\n");
+
+					} catch (IOException e) {
+						e.printStackTrace();
+					}
 				}
-				System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";EXPORT;"
-						+ basin.getName() + "; " + totalOutputFluxes);
 			}
 		}
-		
-		
 	}
 }
\ No newline at end of file

src/main/java/species/ReproduceAndSurviveAfterReproductionWithDiagnose.java

 package species;
 
 
+import java.io.BufferedWriter;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Hashtable;
@@ -59,9 +61,13 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 	private double maxNumberOfSuperIndividualPerReproduction = 50.;
 	private boolean withDiagnose = true;
 
+	private boolean displayFluxesOnConsole = true;
+
 
 	private transient NormalGen genNormal;
 	private transient MortalityFunction mortalityFunction;
+
+	private  enum fluxOrigin {AUTOCHTONOUS, ALLOCHTONOUS};
 	/**
 	 *  relationship between
 	 *  	recruitment in number of juvenile on spawning grounds
@@ -110,10 +116,10 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 				if (fishInBasin != null){
 
 					//Initiate the total fluxes for this basin 
-					Map<String, Map<String, Double>> totalInputFluxes = new Hashtable<String, Map <String, Double>>(); //On crer la Map pour stocker les flux 
-					totalInputFluxes.put("autochtonous", new Hashtable < String, Double>()); 
-					totalInputFluxes.put("allochtonous", new Hashtable < String, Double>()); 
-					for (String origin: totalInputFluxes.keySet()) {
+					Map<fluxOrigin, Map<String, Double>> totalInputFluxes = new Hashtable<fluxOrigin, Map <String, Double>>(); //On cr�er la Map pour stocker les flux 
+					totalInputFluxes.put(fluxOrigin.AUTOCHTONOUS, new Hashtable < String, Double>()); 
+					totalInputFluxes.put(fluxOrigin.ALLOCHTONOUS, new Hashtable < String, Double>()); 
+					for (fluxOrigin origin: totalInputFluxes.keySet()) {
 						for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
 							totalInputFluxes.get(origin).put(nutrient, 0.); // ON MET A JOUR NOTRE map 
 						}
@@ -195,11 +201,11 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 							// survival after reproduction (semelparity or iteroparity) of SI (change the amount of the SI)
 							survivalAmount = Miscellaneous.binomialForSuperIndividual(group.getPilot(), fish.getAmount(), survivalRateAfterReproduction); 
 							double biomass = 0.; 
-							String origin; 
+							fluxOrigin origin; 
 							if(fish.getBirthBasin()== riverBasin) 
-								origin = "autochtonous"; 
+								origin = fluxOrigin.AUTOCHTONOUS; 
 							else
-								origin = "allochtonous"; 
+								origin = fluxOrigin.ALLOCHTONOUS;
 							if (survivalAmount > 0) {// SUperindividu est encore vivant mais il perd des effectifs 
 
 								//Export for fishes survived after spawning (survivalAmount) : excretion + gametes
@@ -395,9 +401,28 @@ public class ReproduceAndSurviveAfterReproductionWithDiagnose extends AquaNismsG
 					}
 					deadFish.clear();
 
-					System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
-							+ riverBasin.getName() + "; " + totalInputFluxes);
 
+					if 	(displayFluxesOnConsole)
+						System.out.println(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) + ";IMPORT;"
+								+ riverBasin.getName() + "; " + totalInputFluxes);
+
+					BufferedWriter bW = group.getbWForFluxes();
+					if ( bW != null) {
+						try {
+							for (fluxOrigin origin : totalInputFluxes.keySet()) {
+								bW.write(group.getPilot().getCurrentTime() + "; " + Time.getYear(group.getPilot()) + ";" + Time.getSeason(group.getPilot()) 
+								+";"+ riverBasin.getName() +  ";IMPORT;"+origin);
+								bW.write(";" + totalInputFluxes.get(origin).get("biomass"));
+								for (String nutrient : group.getNutrientRoutine().getNutrientsOfInterest()) {
+									bW.write(";" + totalInputFluxes.get(origin).get(nutrient));
+								}
+								bW.write("\n");
+							}
+						} catch (IOException e) {
+
+							e.printStackTrace();
+						}
+					}
 				}
 				else {
 					riverBasin.setYearOfLastNulRep(Time.getYear(group.getPilot()));