mobe getSimultationId from group to BainNetwork

src/main/java/analysis/ExportExchangeSBetweenCatchments.java

@@ -159,8 +159,8 @@ public class ExportExchangeSBetweenCatchments extends AquaNismsGroupProcess<Diad
 				sep = ",";
 				try {
 					new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
-					bW = new BufferedWriter(
-							new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
+					bW = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameOutput + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bW.write("year" + sep + "migrationBasin" + sep + "natalBasin" + sep + "effective");
 					bW.write("\n");

src/main/java/analysis/ExportLenghtAgeDistribution.java

@@ -33,8 +33,8 @@ import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
 import species.DiadromousFish;
-import species.DiadromousFishGroup;
 import species.DiadromousFish.Stage;
+import species.DiadromousFishGroup;
 
 /**
  *
@@ -46,35 +46,40 @@ public class ExportLenghtAgeDistribution extends AquaNismsGroupProcess<Diadromou
 	private String fileNameOutput = "lengthAgeDistribution";
 
 	private transient BufferedWriter bW;
-	private transient String sep=";";
+	private transient String sep = ";";
 
 	public static void main(String[] args) {
-		System.out.println((new XStream(new DomDriver()))
-				.toXML(new ExportLenghtAgeDistribution()));
+		System.out.println((new XStream(new DomDriver())).toXML(new ExportLenghtAgeDistribution()));
 	}
 
-	/* (non-Javadoc)
-	 * @see fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess#initTransientParameters(fr.cemagref.simaqualife.pilot.Pilot)
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see
+	 * fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess#initTransientParameters(fr.cemagref.simaqualife.
+	 * pilot.Pilot)
 	 */
 	@Override
 	public void initTransientParameters(Pilot pilot) {
 		super.initTransientParameters(pilot);
-		sep=";";
+		sep = ";";
 
 	}
 
+
 	@Override
 	public void doProcess(DiadromousFishGroup group) {
 
-		if (bW==null){
-			if (fileNameOutput != null){
-				new File(group.getOutputPath()+fileNameOutput).getParentFile().mkdirs();
+		if (bW == null) {
+			if (fileNameOutput != null) {
+				new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
 				try {
-					bW = new BufferedWriter(new FileWriter(new File(group.getOutputPath()+
-							fileNameOutput +group.getSimulationId()+ ".csv")));
+					bW = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameOutput + group.getEnvironment().getSimulationId() + ".csv")));
 
-					bW.write("timestep"+sep+"year"+sep+"season"+sep+"basin"+ sep+"gender" 
-							+sep+ "effective" +sep+"length"+sep+"age"+sep+"nbSpawn"+"\n");
+					bW.write("timestep" + sep + "year" + sep + "season" + sep + "basin" + sep + "gender" + sep + "effective" + sep
+							+ "length" + sep + "age" + sep + "nbSpawn" + "\n");
 
 				} catch (IOException e) {
 					e.printStackTrace();
@@ -84,14 +89,15 @@ public class ExportLenghtAgeDistribution extends AquaNismsGroupProcess<Diadromou
 
 		try {
 			Time time = group.getEnvironment().getTime();
-			if (time.getSeason(pilot) == exportSeason & time.getYear(pilot)>1900) {
+			if (time.getSeason(pilot) == exportSeason & time.getYear(pilot) > 1900) {
 				for (RiverBasin basin : group.getEnvironment().getRiverBasins()) {
 					if (basin.getFishs(group) != null) {
 						for (DiadromousFish fish : basin.getFishs(group)) {
 							if (fish.getStage() == Stage.MATURE) {
-								
-								//System.out.println(fish.getAge() + " -> "+ fish.getLength() +" - "+fish.getNumberOfReproduction());
-								
+
+								// System.out.println(fish.getAge() + " -> "+ fish.getLength() +" -
+								// "+fish.getNumberOfReproduction());
+
 								bW.write(pilot.getCurrentTime() + sep);
 								bW.write(time.getYear(pilot) + sep);
 								bW.write(time.getSeason(pilot) + sep);
@@ -99,18 +105,17 @@ public class ExportLenghtAgeDistribution extends AquaNismsGroupProcess<Diadromou
 								bW.write(fish.getGender() + sep);
 								bW.write(fish.getAmount() + sep);
 								bW.write(fish.getLength() + sep);
-								bW.write(fish.getAge()+ sep);
-								bW.write(fish.getNumberOfReproduction()+	"\n");
+								bW.write(fish.getAge() + sep);
+								bW.write(fish.getNumberOfReproduction() + "\n");
 							}
 						}
 					}
 				}
 			}
-			if (group.getPilot().getCurrentTime()== group.getPilot().getSimBegin()+group.getPilot().getSimDuration()-1)
+			if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin() + group.getPilot().getSimDuration() - 1)
 				bW.close();
 		} catch (IOException e) {
 			e.printStackTrace();
 		}
 	}
 }
-

src/main/java/analysis/ExportMeanRecruitment.java

@@ -45,8 +45,8 @@ public class ExportMeanRecruitment extends AquaNismsGroupProcess<DiadromousFish,
 			if (fileNameOutput != null) {
 				try {
 					new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
-					bW = new BufferedWriter(
-							new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
+					bW = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameOutput + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bW.write("timestep" + sep + "year" + sep + "season");
 

src/main/java/analysis/ExportPopulationStatus.java

@@ -50,8 +50,8 @@ public class ExportPopulationStatus extends AquaNismsGroupProcess<DiadromousFish
 				if (bWMortality == null) {
 
 					new File(group.getOutputPath() + fileNameMortality).getParentFile().mkdirs();
-					bWMortality = new BufferedWriter(new FileWriter(
-							new File(group.getOutputPath() + fileNameMortality + group.getSimulationId() + ".csv")));
+					bWMortality = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameMortality + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bWMortality.write("timestep" + sep + "year" + sep + "season");
 
@@ -66,8 +66,8 @@ public class ExportPopulationStatus extends AquaNismsGroupProcess<DiadromousFish
 				if (bWMortalityCrash == null) {
 
 					new File(group.getOutputPath() + fileNameMortalityCrash).getParentFile().mkdirs();
-					bWMortalityCrash = new BufferedWriter(new FileWriter(
-							new File(group.getOutputPath() + fileNameMortalityCrash + group.getSimulationId() + ".csv")));
+					bWMortalityCrash = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameMortalityCrash + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bWMortalityCrash.write("timestep" + sep + "year" + sep + "season");
 
@@ -82,8 +82,8 @@ public class ExportPopulationStatus extends AquaNismsGroupProcess<DiadromousFish
 				if (bWStockTrap == null) {
 
 					new File(group.getOutputPath() + fileNameStockTrap).getParentFile().mkdirs();
-					bWStockTrap = new BufferedWriter(new FileWriter(
-							new File(group.getOutputPath() + fileNameStockTrap + group.getSimulationId() + ".csv")));
+					bWStockTrap = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameStockTrap + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bWStockTrap.write("timestep" + sep + "year" + sep + "season");
 
@@ -98,8 +98,8 @@ public class ExportPopulationStatus extends AquaNismsGroupProcess<DiadromousFish
 				if (bwPopulationStatus == null) {
 
 					new File(group.getOutputPath() + fileNamePopulationStatus).getParentFile().mkdirs();
-					bwPopulationStatus = new BufferedWriter(new FileWriter(
-							new File(group.getOutputPath() + fileNamePopulationStatus + group.getSimulationId() + ".csv")));
+					bwPopulationStatus = new BufferedWriter(new FileWriter(new File(group.getOutputPath()
+							+ fileNamePopulationStatus + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bwPopulationStatus.write("timestep" + sep + "year" + sep + "season");
 

src/main/java/analysis/ExportRecruitment.java

@@ -43,8 +43,8 @@ public class ExportRecruitment extends AquaNismsGroupProcess<DiadromousFish, Dia
 			if (fileNameOutput != null) {
 				try {
 					new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
-					bW = new BufferedWriter(
-							new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
+					bW = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameOutput + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bW.write("timestep" + sep + "year" + sep + "season");
 

src/main/java/analysis/ExportSpeciesRange.java

@@ -84,8 +84,8 @@ public class ExportSpeciesRange extends AquaNismsGroupProcess<DiadromousFish, Di
 			if (fileNameOutput != null) {
 				new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
 				try {
-					bW = new BufferedWriter(
-							new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
+					bW = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameOutput + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bW.write("timestep" + sep + "year" + sep + "season" + sep + "medianRange" + sep + "southRange" + sep
 							+ "northRange" + sep + "centileRange" + "\n");

src/main/java/analysis/TypeTrajectoryCV.java

@@ -235,8 +235,8 @@ public class TypeTrajectoryCV extends AquaNismsGroupProcess<DiadromousFish, Diad
 			new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
 
 			try {
-				bW = new BufferedWriter(
-						new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
+				bW = new BufferedWriter(new FileWriter(
+						new File(group.getOutputPath() + fileNameOutput + group.getEnvironment().getSimulationId() + ".csv")));
 				int nbBV = finalStatesNames.length;
 
 				bW.write("nom des bv");

src/main/java/analysis/WriteBiomassFluxes.java

@@ -16,8 +16,8 @@ import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
 import species.DiadromousFish;
-import species.DiadromousFishGroup;
 import species.DiadromousFish.Stage;
+import species.DiadromousFishGroup;
 
 /**
  *
@@ -31,7 +31,6 @@ public class WriteBiomassFluxes extends AquaNismsGroupProcess<DiadromousFish, Di
 	private transient BufferedWriter bW;
 	private transient String sep = ";";
 
-
 	public static void main(String[] args) {
 		System.out.println((new XStream(new DomDriver())).toXML(new WriteBiomassFluxes()));
 	}
@@ -58,8 +57,8 @@ public class WriteBiomassFluxes extends AquaNismsGroupProcess<DiadromousFish, Di
 			if (fileNameOutput != null) {
 				new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
 				try {
-					bW = new BufferedWriter(
-							new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
+					bW = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameOutput + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bW.write("year" + sep + "migrationBasin"); // create the field of the column
 					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {

src/main/java/analysis/WriteCurrentNutrientExportFluxes.java

@@ -22,7 +22,6 @@ public class WriteCurrentNutrientExportFluxes extends AquaNismsGroupProcess<Diad
 
 	private transient BufferedWriter bW;
 
-
 	public static void main(String[] args) {
 		System.out.println((new XStream(new DomDriver())).toXML(new WriteCurrentNutrientExportFluxes()));
 	}
@@ -41,7 +40,7 @@ public class WriteCurrentNutrientExportFluxes extends AquaNismsGroupProcess<Diad
 				new File(outputPath + fileName).getParentFile().mkdirs();
 
 				bW = new BufferedWriter(
-						new FileWriter(new File(outputPath + fileName + group.getSimulationId() + ".csv")));
+						new FileWriter(new File(outputPath + fileName + group.getEnvironment().getSimulationId() + ".csv")));
 
 				bW.write("year" + sep + "nutrient" + sep + "originBasin" + sep + "value" + "\n");
 			}
@@ -64,8 +63,7 @@ public class WriteCurrentNutrientExportFluxes extends AquaNismsGroupProcess<Diad
 			}
 
 			// close the bW
-			if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin() + group.getPilot().getSimDuration()
-					- 1) {
+			if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin() + group.getPilot().getSimDuration() - 1) {
 				bW.flush();
 				bW.close();
 			}

src/main/java/analysis/WriteCurrentNutrientImportFluxes.java

@@ -22,7 +22,6 @@ public class WriteCurrentNutrientImportFluxes extends AquaNismsGroupProcess<Diad
 
 	private transient BufferedWriter bW;
 
-
 	public static void main(String[] args) {
 		System.out.println((new XStream(new DomDriver())).toXML(new WriteCurrentNutrientImportFluxes()));
 
@@ -43,7 +42,7 @@ public class WriteCurrentNutrientImportFluxes extends AquaNismsGroupProcess<Diad
 				new File(outputPath + fileName).getParentFile().mkdirs();
 
 				bW = new BufferedWriter(
-						new FileWriter(new File(outputPath + fileName + group.getSimulationId() + ".csv")));
+						new FileWriter(new File(outputPath + fileName + group.getEnvironment().getSimulationId() + ".csv")));
 
 				bW.write("year" + sep + "nutrient" + sep + "originBasin");
 				for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
@@ -78,8 +77,7 @@ public class WriteCurrentNutrientImportFluxes extends AquaNismsGroupProcess<Diad
 			}
 
 			// close the bW
-			if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin() + group.getPilot().getSimDuration()
-					- 1) {
+			if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin() + group.getPilot().getSimDuration() - 1) {
 				bW.flush();
 				bW.close();
 			}

src/main/java/analysis/WriteEffectiveAndBiomassExportFluxes.java

@@ -4,7 +4,6 @@ import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
-import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.ListIterator;
@@ -18,8 +17,8 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import species.DiadromousFish;
-import species.DiadromousFishGroup;
 import species.DiadromousFish.Stage;
+import species.DiadromousFishGroup;
 
 public class WriteEffectiveAndBiomassExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
 
@@ -46,40 +45,40 @@ public class WriteEffectiveAndBiomassExportFluxes extends AquaNismsGroupProcess<
 				new File(outputPath + fileName).getParentFile().mkdirs();
 
 				bW = new BufferedWriter(
-						new FileWriter(new File(outputPath + fileName + group.getSimulationId() + ".csv")));
+						new FileWriter(new File(outputPath + fileName + group.getEnvironment().getSimulationId() + ".csv")));
 
 				bW.write("year" + sep + "originBasin" + sep + "abundance" + sep + "biomass" + "\n");
 			}
 
 			// write information for the current year
-			Map<String, Double> totalOutputFluxes = new Hashtable<String, Double>(); 
+			Map<String, Double> totalOutputFluxes = new Hashtable<String, Double>();
 
 			long year = time.getYear(group.getPilot());
 
-			if (year >= group.getMinYearToWrite() & time.getSeason(group.getPilot()) == writeSeason) {			
-				for (RiverBasin basin : group.getEnvironment().getRiverBasins()){
+			if (year >= group.getMinYearToWrite() & time.getSeason(group.getPilot()) == writeSeason) {
+				for (RiverBasin basin : group.getEnvironment().getRiverBasins()) {
 
-					totalOutputFluxes.put("biomass", 0.); //cr�ation de la biomasse 
+					totalOutputFluxes.put("biomass", 0.); // cr�ation de la biomasse
 					totalOutputFluxes.put("abundance", 0.);
 
 					List<DiadromousFish> fishes = basin.getFishs(group);
-					if (fishes!=null) {
+					if (fishes != null) {
 						ListIterator<DiadromousFish> fishIterator = fishes.listIterator();
 						// for (DiadromousFish fish : fishes) {
 						while (fishIterator.hasNext()) {
 							DiadromousFish fish = fishIterator.next();
-							if (fish.getStage()==Stage.IMMATURE) {
+							if (fish.getStage() == Stage.IMMATURE) {
 								double abundanceExp = fish.getAmount();
-								double biomass = group.getNutrientRoutine().getWeight(fish) * fish.getAmount(); 
-								totalOutputFluxes.put("biomass", totalOutputFluxes.get("biomass") + biomass); 
-								totalOutputFluxes.put("abundance", totalOutputFluxes.get("abundance") + abundanceExp); 
-							}	
+								double biomass = group.getNutrientRoutine().getWeight(fish) * fish.getAmount();
+								totalOutputFluxes.put("biomass", totalOutputFluxes.get("biomass") + biomass);
+								totalOutputFluxes.put("abundance", totalOutputFluxes.get("abundance") + abundanceExp);
+							}
 						}
 					}
 					try {
 
-						bW.write(time.getYear(group.getPilot()) + ";"+ basin.getName() + ";");
-						bW.write(+ totalOutputFluxes.get("abundance") + ";" + totalOutputFluxes.get("biomass"));
+						bW.write(time.getYear(group.getPilot()) + ";" + basin.getName() + ";");
+						bW.write(+totalOutputFluxes.get("abundance") + ";" + totalOutputFluxes.get("biomass"));
 						bW.write("\n");
 
 					} catch (IOException e) {
@@ -89,8 +88,7 @@ public class WriteEffectiveAndBiomassExportFluxes extends AquaNismsGroupProcess<
 			}
 
 			// close the bW
-			if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin() + group.getPilot().getSimDuration()
-					- 1) {
+			if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin() + group.getPilot().getSimDuration() - 1) {
 				bW.flush();
 				bW.close();
 			}

src/main/java/analysis/WriteEffectiveAndBiomassImportFluxes.java

@@ -35,8 +35,8 @@ import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
 import species.DiadromousFish;
-import species.DiadromousFishGroup;
 import species.DiadromousFish.Stage;
+import species.DiadromousFishGroup;
 
 /**
  *
@@ -50,7 +50,6 @@ public class WriteEffectiveAndBiomassImportFluxes extends AquaNismsGroupProcess<
 	private transient BufferedWriter bW;
 	private transient String sep = ";";
 
-
 	public static void main(String[] args) {
 		System.out.println((new XStream(new DomDriver())).toXML(new WriteEffectiveAndBiomassImportFluxes()));
 	}
@@ -78,8 +77,8 @@ public class WriteEffectiveAndBiomassImportFluxes extends AquaNismsGroupProcess<
 			if (fileNameOutput != null) {
 				new File(group.getOutputPath() + fileNameOutput).getParentFile().mkdirs();
 				try {
-					bW = new BufferedWriter(
-							new FileWriter(new File(group.getOutputPath() + fileNameOutput + group.getSimulationId() + ".csv")));
+					bW = new BufferedWriter(new FileWriter(new File(
+							group.getOutputPath() + fileNameOutput + group.getEnvironment().getSimulationId() + ".csv")));
 
 					bW.write("year" + sep + "type" + sep + "originBasin"); // create the field of the column
 					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {

src/main/java/environment/BasinNetwork.java

@@ -83,4 +83,19 @@ public abstract class BasinNetwork extends Environment<Basin, DiadromousFish> {
 
 	}
 
+
+	/**
+	 * 
+	 * concat at RngSatusIndex, temperatureCatchmentFile
+	 * 
+	 * @return simulation name
+	 */
+	public String getSimulationId() {
+		String id = "_";
+		id = id.concat(Integer.toString(getPilot().getParameters().getRngStatusIndex()));
+		String temperatureFile = getTemperatureCatchmentFile();
+		id = id.concat("-").concat(temperatureFile);
+		return id;
+	}
+
 }

src/main/java/species/DiadromousFishGroup.java

@@ -435,8 +435,8 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, RIOBasin
 			sep = ";";
 			new File(this.outputPath + fileNameFluxes).getParentFile().mkdirs();
 			try {
-				bWForFluxes = new BufferedWriter(
-						new FileWriter(new File(this.outputPath + fileNameFluxes + this.getSimulationId() + ".csv")));
+				bWForFluxes = new BufferedWriter(new FileWriter(
+						new File(this.outputPath + fileNameFluxes + this.getEnvironment().getSimulationId() + ".csv")));
 
 				bWForFluxes.write("timestep" + sep + "year" + sep + "season" + sep + "basin" + sep + "abundance" + sep
 						+ "fluxType" + sep + "origin" + sep + "abundanceExp" + sep + "biomass");
@@ -627,24 +627,6 @@ public class DiadromousFishGroup extends AquaNismsGroup<DiadromousFish, RIOBasin
 	}
 
 
-	/**
-	 * 
-	 * concat at RngSatusIndex, temperatureCatchmentFile
-	 * 
-	 * @return simulation name
-	 */
-	public String getSimulationId() {
-		String id = "_";
-		id = id.concat(Integer.toString(getPilot().getParameters().getRngStatusIndex()));
-		String temperatureFile = ((RIOBasinNetwork) getPilot().getAquaticWorld().getEnvironment()).getTemperatureCatchmentFile();
-		id = id.concat("-").concat(temperatureFile);
-		if (parameterSetLine > 0) {
-			id = id.concat("-").concat(Integer.toString(parameterSetLine));
-		}
-		return id;
-	}
-
-
 	public boolean isThereBasinToUpdate() {
 		return basinsToUpdate != null;
 	}