diff --git a/src/main/java/environment/BasinNetwork.java b/src/main/java/environment/BasinNetwork.java index 7254a3f0dce5e7efc78295661a4a57ece447f232..3d24431f56df92e29928969d9229510cdd3c5b93 100644 --- a/src/main/java/environment/BasinNetwork.java +++ b/src/main/java/environment/BasinNetwork.java @@ -32,12 +32,6 @@ public abstract class BasinNetwork extends Environment<Basin, DiadromousFish> { 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); @@ -47,15 +41,9 @@ public abstract class BasinNetwork extends Environment<Basin, DiadromousFish> { public abstract RiverBasin getRiverBasin(String basinName); - public abstract InshoreBasin getInshoreBasin(String riverBasinName); - - public abstract RiverBasin[] getRiverBasins(); - public abstract InshoreBasin[] getInshoreBasins(); - - public abstract String[] getRiverBasinNames(); diff --git a/src/main/java/environment/BasinNetworkWithnBasins.java b/src/main/java/environment/BasinNetworkWithnBasins.java index cf092c271d90feca601a8dcdcf8ad086268a8243..d9633bd1784e15cfa33e7b816a4dbf60c140a850 100644 --- a/src/main/java/environment/BasinNetworkWithnBasins.java +++ b/src/main/java/environment/BasinNetworkWithnBasins.java @@ -14,6 +14,7 @@ import environment.OffshoreBasin.OffshoreBasinFunction; import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters; import fr.cemagref.simaqualife.pilot.Pilot; +@Deprecated public class BasinNetworkWithnBasins extends GridBasinNetwork { private String basinNetworkFileName = "data/input/BasinNetwork.csv"; diff --git a/src/main/java/environment/GridBasinNetwork.java b/src/main/java/environment/GridBasinNetwork.java index 593baa7e885fce8bbe47ccb963b11b4ec7e72b92..357b65f18cf36b097cab1c03a1b79c2eb5f8da28 100644 --- a/src/main/java/environment/GridBasinNetwork.java +++ b/src/main/java/environment/GridBasinNetwork.java @@ -6,12 +6,11 @@ import java.util.Map; import java.util.TreeMap; 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 GridBasinNetwork extends Environment<Basin, DiadromousFish> { +public abstract class GridBasinNetwork extends BasinNetwork { protected int nbBasin; protected int memorySize; // size of all the queues @@ -28,6 +27,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish protected transient Time time; + @Override @InitTransientParameters public void initTransientParameters(Pilot pilot) { time = new Time(); @@ -49,6 +49,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public Basin getAssociatedRiverBasin(Basin basin) { int i = getRow(basin.getId()); return (grid[getId(i, 0)]); @@ -87,6 +88,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public Map<Basin, Double> getNeighboursWithDistance(Basin basin) { int j = getColumn(basin.getId()); if (j == 0) // that means for a river basin @@ -111,11 +113,13 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public Basin[] getBasins() { return grid; } + @Override public RiverBasin getRiverBasin(String basinName) { RiverBasin basin = null; for (int i = 0; i < nbBasin; i++) { @@ -141,6 +145,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public RiverBasin[] getRiverBasins() { RiverBasin[] riverGrid = new RiverBasin[nbBasin]; @@ -163,6 +168,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public String[] getRiverBasinNames() { RiverBasin[] riverBasins = getRiverBasins(); String[] names = new String[riverBasins.length]; @@ -173,6 +179,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public int[] getFinalStates() { // TODO ask to Nicolas to be able to use ReflectUtils with arguments @@ -193,6 +200,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public int[] getFinalStatesWithStochasticity() { // TODO ask to Nicolas to be able to use ReflectUtils with arguments @@ -213,6 +221,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public int[] getFinalStatesForKappa() { // TODO ask to Nicolas to be able to use ReflectUtils with arguments @@ -230,6 +239,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public double[] getMeanLastRecruitments() { RiverBasin[] riverBasins = getRiverBasins(); double[] data = new double[riverBasins.length]; @@ -240,6 +250,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public double[] getProbOfNonNulRecruitmentDuringLastYears() { RiverBasin[] riverBasins = getRiverBasins(); double[] data = new double[riverBasins.length]; @@ -258,6 +269,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public double[] getFinalProbabilityOfPresence() { // function computed for obtain probability of presence in 2100 // for the allis shad case study RiverBasin[] riverBasins = getRiverBasins(); @@ -270,6 +282,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public double getMeanLastRecruitmentsBV2() { RiverBasin[] riverBasins = getRiverBasins(); double data = riverBasins[1].getLastRecruitments().getMean(); @@ -277,6 +290,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public double[] getMeanLastRecruitmentExpectations() { RiverBasin[] riverBasins = getRiverBasins(); double[] data = new double[riverBasins.length]; @@ -287,6 +301,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public double[] getGeoMeansLastRecsOverProdCaps() { // TODO ask to Nicolas to be able to use ReflectUtils with arguments @@ -299,6 +314,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public double[] getMeanLastPercOfAut() { // give the mean of the last % of autochtone spawners RiverBasin[] riverBasins = getRiverBasins(); double[] data = new double[riverBasins.length]; @@ -309,6 +325,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public long[] getYearsOfFirstNonNulRep() { RiverBasin[] riverBasins = getRiverBasins(); long[] data = new long[riverBasins.length]; @@ -319,6 +336,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public long[] getYearsOfLastNulRep() { RiverBasin[] riverBasins = getRiverBasins(); long[] data = new long[riverBasins.length]; @@ -332,6 +350,7 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish /** * @return the yearOfTheBegin */ + @Override public long getYearOfTheBegin() { return yearOfTheBegin; } @@ -355,15 +374,18 @@ public abstract class GridBasinNetwork extends Environment<Basin, DiadromousFish } + @Override public abstract Map<String, Double[]> getTemperaturesBasin(long year); + @Override public abstract String getTemperatureCatchmentFile(); /** * @return the time */ + @Override public Time getTime() { return time; diff --git a/src/main/java/environment/RIOBasinNetwork.java b/src/main/java/environment/RIOBasinNetwork.java index 382149f89d152c08835748388410de6a89654c9f..c31eaa7fea795e526b99224a3154d7d8dc842ec5 100644 --- a/src/main/java/environment/RIOBasinNetwork.java +++ b/src/main/java/environment/RIOBasinNetwork.java @@ -85,7 +85,6 @@ public abstract class RIOBasinNetwork extends BasinNetwork { } - @Override public InshoreBasin[] getInshoreBasins() { return inshoreBasins; } @@ -106,7 +105,6 @@ public abstract class RIOBasinNetwork extends BasinNetwork { } - @Override @Deprecated public Basin getAssociatedOffshoreBasin(Basin basin) { Basin associatedBasin = null; @@ -180,7 +178,6 @@ public abstract class RIOBasinNetwork extends BasinNetwork { } - @Override public InshoreBasin getInshoreBasin(String basinName) { InshoreBasin basin = null; for (InshoreBasin inshoreBasin : inshoreBasins) { diff --git a/src/main/java/environment/RIOBasinNetworkWithContinent.java b/src/main/java/environment/RIOBasinNetworkWithContinent.java index a16b76f95541f75959fa8e3ab616b85322c1e947..4e52acd97797f876377e44a5fccb4c9063ade4c0 100644 --- a/src/main/java/environment/RIOBasinNetworkWithContinent.java +++ b/src/main/java/environment/RIOBasinNetworkWithContinent.java @@ -600,12 +600,4 @@ public class RIOBasinNetworkWithContinent extends RIOBasinNetwork { public Map<String, Path2D.Double> getMapContinent() { return mapContinent; } - - - @Override - @Deprecated - public Basin getAssociatedInshoreBasin(Basin basin) { - // TODO Auto-generated method stub - return null; - } } diff --git a/src/main/java/species/DisperseAndMigrateToRiver.java b/src/main/java/species/DisperseAndMigrateToRiver.java index 44f8c90a96a9acdacea9c968df5387a9fac283dd..27ca49bc4a9f74d7ca3535a13bae54948c181ba1 100644 --- a/src/main/java/species/DisperseAndMigrateToRiver.java +++ b/src/main/java/species/DisperseAndMigrateToRiver.java @@ -17,6 +17,7 @@ import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import miscellaneous.BinomialForSuperIndividualGen; @ServiceProvider(service = AquaNismsGroupProcess.class) +@Deprecated public class DisperseAndMigrateToRiver extends DisperseAndMigrateToRiverBasic { private double pHoming = 0.5; diff --git a/src/main/java/species/DisperseAndMigrateToRiverStandardization.java b/src/main/java/species/DisperseAndMigrateToRiverStandardization.java index 769a0ff5633e854989bb2a1bb9eb9a7e8fd98da1..47aae48ce8ac9f748ee600de955c81ff0f0ecb64 100644 --- a/src/main/java/species/DisperseAndMigrateToRiverStandardization.java +++ b/src/main/java/species/DisperseAndMigrateToRiverStandardization.java @@ -23,6 +23,7 @@ import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientPara import fr.cemagref.simaqualife.pilot.Pilot; import miscellaneous.BinomialForSuperIndividualGen; +@Deprecated @ServiceProvider(service = AquaNismsGroupProcess.class) public class DisperseAndMigrateToRiverStandardization extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> { @@ -129,7 +130,7 @@ public class DisperseAndMigrateToRiverStandardization extends AquaNismsGroupProc // distance from departure basin to destination basin Map<RiverBasin, Double> distanceBasinFromDeparture = basinDistancesPerBasin.get(departure); - RiverBasin homingDestination = (RiverBasin) bn.getAssociatedRiverBasin(departure); + RiverBasin homingDestination = bn.getAssociatedRiverBasin(departure); ListIterator<DiadromousFish> fishIterator = departure.getFishs(group).listIterator(); while (fishIterator.hasNext()) { diff --git a/src/main/java/species/WriteNutrientExportFluxes.java b/src/main/java/species/WriteNutrientExportFluxes.java index b9c863a62c56b0d317701c14f313c2629d4936ae..3ab9320febddb43a3855d50a240ec36d0cb730fe 100644 --- a/src/main/java/species/WriteNutrientExportFluxes.java +++ b/src/main/java/species/WriteNutrientExportFluxes.java @@ -14,6 +14,7 @@ import com.thoughtworks.xstream.io.xml.DomDriver; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; +@Deprecated public class WriteNutrientExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> { private String fileName = "nutrientExportFluxes"; diff --git a/src/main/java/species/WriteNutrientImportFluxes.java b/src/main/java/species/WriteNutrientImportFluxes.java index 5418cf1bbdeca05423585abd04a63c2354c83dbd..127f05a169d81268421e2d69e4f38e3c0039b772 100644 --- a/src/main/java/species/WriteNutrientImportFluxes.java +++ b/src/main/java/species/WriteNutrientImportFluxes.java @@ -14,6 +14,7 @@ import com.thoughtworks.xstream.io.xml.DomDriver; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; +@Deprecated public class WriteNutrientImportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> { private String fileName = "fluxes";