fix jet pilot + code cleaning

src/main/java/species/WriteBiomassFluxes.java

@@ -5,8 +5,6 @@ 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.Map;
 
 import com.thoughtworks.xstream.XStream;
@@ -17,55 +15,57 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
-import miscellaneous.Miscellaneous;
 import species.DiadromousFish.Stage;
-import species.ReproduceAndSurviveAfterReproductionWithDiagnose;
 
 /**
  *
  */
 public class WriteBiomassFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
 
-
 	private Season exportSeason = Season.SPRING;
 
 	private String fileNameOutput = "biomassFluxes";
 
 	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 WriteBiomassFluxes()));
+		System.out.println((new XStream(new DomDriver())).toXML(new WriteBiomassFluxes()));
 	}
 
-	/* (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=";";
-
 	}
 
+
 	@Override
 	public void doProcess(DiadromousFishGroup group) {
 
-		if (bW==null){
-			if (fileNameOutput != null){
-				new File(group.getOutputPath()+fileNameOutput).getParentFile().mkdirs();
+		if (bW == null) {
+			sep = ";";
+			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.getSimulationId() + ".csv")));
 
-					bW.write("year"+sep+"migrationBasin" ); //create the field of the column
+					bW.write("year" + sep + "migrationBasin"); // create the field of the column
 					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
-						bW.write(sep + birthBasinName); // write each basin name in the file 
+						bW.write(sep + birthBasinName); // write each basin name in the file
 					}
 
-					bW.write("\n"); 
+					bW.write("\n");
+					bW.flush();
 
 				} catch (IOException e) {
 					e.printStackTrace();
@@ -75,17 +75,19 @@ public class WriteBiomassFluxes extends AquaNismsGroupProcess<DiadromousFish, Di
 
 		try {
 			Time time = group.getEnvironment().getTime();
-			if (time.getSeason(pilot) == exportSeason & time.getYear(pilot) >= 	group.getMinYearToWrite()) {
-
+			System.out.println(time.getSeason(group.getPilot()));
+			System.out.println(time.getYear(group.getPilot()));
+			if (time.getSeason(group.getPilot()) == exportSeason & time.getYear(group.getPilot()) >= group.getMinYearToWrite()) {
 
 				for (RiverBasin migrationBasin : group.getEnvironment().getRiverBasins()) {
-					//Create the map to get the biomass in each birth basin
-					Map<String, Double> spawnerAbundancesPerOrigin = new HashMap<String, Double>(group.getEnvironment().getRiverBasinNames().length); 
-					for (String basinName : group.getEnvironment().getRiverBasinNames()){
-						spawnerAbundancesPerOrigin.put(basinName,  0.);			
+					// Create the map to get the biomass in each birth basin
+					Map<String, Double> spawnerAbundancesPerOrigin = new HashMap<String, Double>(
+							group.getEnvironment().getRiverBasinNames().length);
+					for (String basinName : group.getEnvironment().getRiverBasinNames()) {
+						spawnerAbundancesPerOrigin.put(basinName, 0.);
 					}
-					double biomass=0.;
-					//compute the cumulative effective per birth basin 
+					double biomass = 0.;
+					// compute the cumulative effective per birth basin
 					if (migrationBasin.getFishs(group) != null) {
 
 						for (DiadromousFish fish : migrationBasin.getFishs(group)) {
@@ -93,24 +95,28 @@ public class WriteBiomassFluxes extends AquaNismsGroupProcess<DiadromousFish, Di
 							if (fish.getStage() == Stage.MATURE) {
 								biomass = group.getNutrientRoutine().getWeight(fish) * fish.getAmount();
 								String birthBasinName = fish.getBirthBasin().getName();
-								spawnerAbundancesPerOrigin.put(birthBasinName, spawnerAbundancesPerOrigin.get(birthBasinName) + biomass);
+								spawnerAbundancesPerOrigin.put(birthBasinName,
+										spawnerAbundancesPerOrigin.get(birthBasinName) + biomass);
 							}
 						}
 					}
 
-					//write the first two fields of the line 
-					bW.write(time.getYear(pilot)+sep+migrationBasin.getName());
+					// write the first two fields of the line
+					bW.write(time.getYear(group.getPilot()) + sep + migrationBasin.getName());
 
-					//write the cumulative effective from birth basin 
+					// write the cumulative effective from birth basin
 					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
-						bW.write(sep+spawnerAbundancesPerOrigin.get(birthBasinName));
+						bW.write(sep + spawnerAbundancesPerOrigin.get(birthBasinName));
 					}
-					//write an end-of(line
+					// write an end-of(line
 					bW.write("\n");
 				}
 			}
-			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();
+			}
+
 		} catch (IOException e) {
 			e.printStackTrace();
 		}

src/main/java/species/WriteEffectiveAndBiomassImportFluxes.java

@@ -76,8 +76,8 @@ 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.getSimulationId() + ".csv")));
 
 					bW.write("year" + sep + "type" + sep + "originBasin"); // create the field of the column
 					for (String birthBasinName : group.getEnvironment().getRiverBasinNames()) {
@@ -93,7 +93,7 @@ public class WriteEffectiveAndBiomassImportFluxes extends AquaNismsGroupProcess<
 
 		Time time = group.getEnvironment().getTime();
 
-		if (time.getSeason(pilot) == exportSeason & time.getYear(pilot) >= group.getMinYearToWrite()) {
+		if (time.getSeason(group.getPilot()) == exportSeason & time.getYear(group.getPilot()) >= group.getMinYearToWrite()) {
 
 			// Create the map to get the biomass in each migration basin and birth basin
 			Map<String, Map<String, Long>> spawnerEffectivePerDestination = new HashMap<String, Map<String, Long>>(
@@ -130,8 +130,7 @@ public class WriteEffectiveAndBiomassImportFluxes extends AquaNismsGroupProcess<
 
 							double biomass = group.getNutrientRoutine().getWeight(fish) * fish.getAmount();
 							spawnerBiomassPerDestination.get(destinationBasin.getName()).put(originBasinName,
-									spawnerBiomassPerDestination.get(destinationBasin.getName()).get(originBasinName)
-											+ biomass);
+									spawnerBiomassPerDestination.get(destinationBasin.getName()).get(originBasinName) + biomass);
 						}
 					}
 				}
@@ -160,8 +159,7 @@ public class WriteEffectiveAndBiomassImportFluxes extends AquaNismsGroupProcess<
 					bW.write("\n");
 				}
 
-				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();
 				}