From d296ad384e62005e25c557f9c91f5da239899dcb Mon Sep 17 00:00:00 2001
From: "patrick.lambert" <patrick.mh.lambert@inrae.fr>
Date: Sat, 5 Dec 2020 08:56:06 +0100
Subject: [PATCH] add @ to depcrecated classes
---
src/main/java/environment/BasinNetwork.java | 12 ---------
.../environment/BasinNetworkWithnBasins.java | 1 +
.../java/environment/GridBasinNetwork.java | 26 +++++++++++++++++--
.../java/environment/RIOBasinNetwork.java | 3 ---
.../RIOBasinNetworkWithContinent.java | 8 ------
.../species/DisperseAndMigrateToRiver.java | 1 +
...perseAndMigrateToRiverStandardization.java | 3 ++-
.../species/WriteNutrientExportFluxes.java | 1 +
.../species/WriteNutrientImportFluxes.java | 1 +
9 files changed, 30 insertions(+), 26 deletions(-)
diff --git a/src/main/java/environment/BasinNetwork.java b/src/main/java/environment/BasinNetwork.java
index 7254a3f..3d24431 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 cf092c2..d9633bd 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 593baa7..357b65f 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 382149f..c31eaa7 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 a16b76f..4e52acd 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 44f8c90..27ca49b 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 769a0ff..47aae48 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 b9c863a..3ab9320 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 5418cf1..127f05a 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";
--
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