Develop a new class for biomass and abundance exports fluxes

data/input/atlanticarea/fishTryRealBV_CC_Alosa.xml

@@ -307,7 +307,13 @@
 					<exportSeason>SPRING</exportSeason>
 					<fileNameOutput>effectiveBiomassFluxesAfterReproduction</fileNameOutput>
 				</species.WriteEffectiveAndBiomassFluxes>
-				
+
+				<species.WriteEffectiveAndBiomassExportFluxes>
+					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
+					<fileName>effectiveAndBiomassExportFluxes</fileName>
+					<writeSeason>SUMMER</writeSeason>
+				</species.WriteEffectiveAndBiomassExportFluxes>
+
 				<species.MigrateToSea>
 					<seaMigrationSeason>SUMMER</seaMigrationSeason>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>

src/main/java/species/WriteEffectiveAndBiomassExportFluxes.java

+package species;
+
+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;
+import java.util.Map;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.DomDriver;
+
+import environment.RiverBasin;
+import environment.Time;
+import environment.Time.Season;
+import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import species.DiadromousFish.Stage;
+
+public class WriteEffectiveAndBiomassExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+
+	private String fileName = "currentEffectiveAndBiomassExportFluxes";
+	private Season writeSeason = Season.SUMMER;
+
+	private transient BufferedWriter bW;
+
+	public static void main(String[] args) {
+		System.out.println((new XStream(new DomDriver())).toXML(new WriteEffectiveAndBiomassExportFluxes()));
+	}
+
+
+	@Override
+	public void doProcess(DiadromousFishGroup group) {
+		String sep = ";";
+
+		Time time = group.getEnvironment().getTime();
+
+		// initialise the bW the first time
+		try {
+			if (bW == null) {
+				String outputPath = group.getOutputPath();
+				new File(outputPath + fileName).getParentFile().mkdirs();
+
+				bW = new BufferedWriter(
+						new FileWriter(new File(outputPath + fileName + group.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>(); 
+
+			long year = time.getYear(group.getPilot());
+
+			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("abundance", 0.);
+
+					List<DiadromousFish> fishes = basin.getFishs(group);
+					if (fishes!=null) {
+						ListIterator<DiadromousFish> fishIterator = fishes.listIterator();
+						// for (DiadromousFish fish : fishes) {
+						while (fishIterator.hasNext()) {
+							DiadromousFish fish = fishIterator.next();
+							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); 
+							}
+						}
+					}
+					try {
+
+						bW.write(time.getYear(group.getPilot()) + ";"+ basin.getName() + ";");
+						bW.write(+ totalOutputFluxes.get("abundance") + ";" + totalOutputFluxes.get("biomass"));
+						bW.write("\n");
+
+					} catch (IOException e) {
+						e.printStackTrace();
+					}
+				}
+			}
+
+			// close the bW
+			if (group.getPilot().getCurrentTime() == group.getPilot().getSimBegin() + group.getPilot().getSimDuration()
+					- 1) {
+				bW.flush();
+				bW.close();
+			}
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+}