with an abstract mother class

src/main/java/environment/BasinNetwork.java

+package environment;
+
+import java.util.Map;
+
+import fr.cemagref.simaqualife.kernel.AquaNismsGroup;
+import fr.cemagref.simaqualife.kernel.spatial.Environment;
+import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
+import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+
+public abstract class BasinNetwork extends Environment<Basin, DiadromousFish> {
+
+	protected int memorySize; // size of all the queues
+	protected int memorySizeLongQueue; // size of all longer queues
+
+	protected double cVthresholdForFinalStates = 5.;
+	protected double RecruitmentThresholdForFsAndKappa = 50.;
+
+	protected long yearOfTheBegin = 1800;
+
+	protected transient double[][] distanceGrid;
+
+	protected transient Time time;
+
+
+	@InitTransientParameters
+	public void initTransientParameters(Pilot pilot) {
+		time = new Time();
+	}
+
+
+	public abstract Basin getAssociatedRiverBasin(Basin basin);
+
+
+	public abstract Basin getAssociatedInshoreBasin(Basin basin);
+
+
+	public abstract Basin getAssociatedOffshoreBasin(Basin basin);
+
+
+	public abstract Map<Basin, Double> getNeighboursWithDistance(Basin basin);
+
+
+	public abstract Basin[] getBasins();
+
+
+	public abstract RiverBasin getRiverBasin(String basinName);
+
+
+	public abstract InshoreBasin getInshoreBasin(String riverBasinName);
+
+
+	public abstract RiverBasin[] getRiverBasins();
+
+
+	public abstract InshoreBasin[] getInshoreBasins();
+
+
+	public abstract String[] getRiverBasinNames();
+
+
+	public int[] getFinalStates() {
+		// TODO ask to Nicolas to be able to use ReflectUtils with arguments
+
+		RiverBasin[] riverBasins = getRiverBasins();
+		int[] finalStates = new int[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			RiverBasin riverBasin = riverBasins[i];
+			double roundedCV = Math.round(riverBasin.getLastRecruitments().getCoefficientVariation() * 10000.) / 100.;
+			if (roundedCV == 0.) {
+				finalStates[i] = 0;
+			} else if (roundedCV < this.cVthresholdForFinalStates) {
+				finalStates[i] = 2;
+			} else {
+				finalStates[i] = 1;
+			}
+		}
+		return finalStates;
+	}
+
+
+	public int[] getFinalStatesWithStochasticity() {
+		// TODO ask to Nicolas to be able to use ReflectUtils with arguments
+
+		RiverBasin[] riverBasins = getRiverBasins();
+		int[] finalStates = new int[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			RiverBasin riverBasin = riverBasins[i];
+			double roundedCV = Math.round(riverBasin.getLastRecruitmentExpectations().getCoefficientVariation() * 10000.) / 100.;
+			if (roundedCV == 0.) {
+				finalStates[i] = 0;
+			} else if (roundedCV < this.cVthresholdForFinalStates) {
+				finalStates[i] = 2;
+			} else {
+				finalStates[i] = 1;
+			}
+		}
+		return finalStates;
+	}
+
+
+	public int[] getFinalStatesForKappa() {
+		// TODO ask to Nicolas to be able to use ReflectUtils with arguments
+
+		RiverBasin[] riverBasins = getRiverBasins();
+		int[] finalStatesForKappa = new int[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			RiverBasin riverBasin = riverBasins[i];
+			if (riverBasin.getLastRecruitments().getMean() <= RecruitmentThresholdForFsAndKappa) {
+				finalStatesForKappa[i] = 0;
+			} else {
+				finalStatesForKappa[i] = 1;
+			}
+		}
+		return finalStatesForKappa;
+	}
+
+
+	public double[] getMeanLastRecruitments() {
+		RiverBasin[] riverBasins = getRiverBasins();
+		double[] data = new double[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			data[i] = riverBasins[i].getLastRecruitments().getMean();
+		}
+		return data;
+	}
+
+
+	public double[] getProbOfNonNulRecruitmentDuringLastYears() {
+		RiverBasin[] riverBasins = getRiverBasins();
+		double[] data = new double[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			if (riverBasins[i].getNumberOfNonNulRecruitmentDuringLastYears().getSum() < 1.0) {
+				data[i] = 0.001;
+			} else if (riverBasins[i].getNumberOfNonNulRecruitmentDuringLastYears()
+					.getSum() > (riverBasins[i].getNumberOfNonNulRecruitmentDuringLastYears().size() - 1)) {
+				data[i] = 0.999;
+			} else {
+				data[i] = riverBasins[i].getNumberOfNonNulRecruitmentDuringLastYears().getSum()
+						/ (riverBasins[i].getNumberOfNonNulRecruitmentDuringLastYears().size());
+			}
+		}
+		return data;
+	}
+
+
+	public double[] getFinalProbabilityOfPresence() { // function computed for obtain probability of presence in 2100
+														// for the allis shad case study
+		RiverBasin[] riverBasins = getRiverBasins();
+		double[] data = new double[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			data[i] = riverBasins[i].getNumberOfNonNulRecruitmentForFinalProbOfPres().getSum()
+					/ riverBasins[i].getNumberOfNonNulRecruitmentForFinalProbOfPres().size();
+		}
+		return data;
+	}
+
+
+	public double getMeanLastRecruitmentsBV2() {
+		RiverBasin[] riverBasins = getRiverBasins();
+		double data = riverBasins[1].getLastRecruitments().getMean();
+		return data;
+	}
+
+
+	public double[] getMeanLastRecruitmentExpectations() {
+		RiverBasin[] riverBasins = getRiverBasins();
+		double[] data = new double[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			data[i] = riverBasins[i].getLastRecruitmentExpectations().getMean();
+		}
+		return data;
+	}
+
+
+	public double[] getGeoMeansLastRecsOverProdCaps() {
+		// TODO ask to Nicolas to be able to use ReflectUtils with arguments
+
+		RiverBasin[] riverBasins = getRiverBasins();
+		double[] geoMeans = new double[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			geoMeans[i] = riverBasins[i].getLastRecsOverProdCaps().getGeometricMean();
+		}
+		return geoMeans;
+	}
+
+
+	public double[] getMeanLastPercOfAut() { // give the mean of the last % of autochtone spawners
+		RiverBasin[] riverBasins = getRiverBasins();
+		double[] data = new double[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			data[i] = riverBasins[i].getLastPercentagesOfAutochtones().getMean();
+		}
+		return data;
+	}
+
+
+	public long[] getYearsOfFirstNonNulRep() {
+		RiverBasin[] riverBasins = getRiverBasins();
+		long[] data = new long[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			data[i] = riverBasins[i].getYearOfFirstNonNulRep();
+		}
+		return data;
+	}
+
+
+	public long[] getYearsOfLastNulRep() {
+		RiverBasin[] riverBasins = getRiverBasins();
+		long[] data = new long[riverBasins.length];
+		for (int i = 0; i < riverBasins.length; i++) {
+			data[i] = riverBasins[i].getYearOfLastNulRep();
+		}
+		return data;
+	}
+
+
+	/**
+	 * @return the yearOfTheBegin
+	 */
+	public long getYearOfTheBegin() {
+		return yearOfTheBegin;
+	}
+
+
+	@Override
+	public void addAquaNism(DiadromousFish fish, AquaNismsGroup group) {
+		// TODO Auto-generated method stub
+	}
+
+
+	@Override
+	public void moveAquaNism(DiadromousFish fish, AquaNismsGroup group, Basin destination) {
+		// TODO Auto-generated method stub
+	}
+
+
+	@Override
+	public void removeAquaNism(DiadromousFish fish, AquaNismsGroup group) {
+		// TODO Auto-generated method stub
+	}
+
+
+	public abstract Map<String, Double[]> getTemperaturesBasin(long year);
+
+
+	public abstract String getTemperatureCatchmentFile();
+
+
+	/**
+	 * @return the time
+	 */
+	public Time getTime() {
+		return time;
+
+	}
+
+}