diff --git a/src/main/java/environment/BasinNetworkObserverWith2Basins.java b/src/main/java/environment/BasinNetworkObserverWith2Basins.java
index d2ab357863adac93099f916917a50c27145d3be8..0de33be6b2b9bd5d364c8ea7fb82121107259142 100644
--- a/src/main/java/environment/BasinNetworkObserverWith2Basins.java
+++ b/src/main/java/environment/BasinNetworkObserverWith2Basins.java
@@ -18,44 +18,42 @@ import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JPanel;
-import species.DiadromousFish;
-import species.DiadromousFishGroup;
-
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.Basin.BasinType;
import fr.cemagref.observation.gui.Configurable;
import fr.cemagref.observation.gui.Drawable;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
@SuppressWarnings("serial")
-public class BasinNetworkObserverWith2Basins extends BasinNetworkObserver implements Configurable,
-Drawable, MouseMotionListener {
+@Deprecated
+public class BasinNetworkObserverWith2Basins extends BasinNetworkObserver implements Configurable, Drawable, MouseMotionListener {
- private double maxDistance =1000.;
+ private double maxDistance = 1000.;
private double minDistance = 50.;
- private double maxSurface=100000.;
-
+ private double maxSurface = 100000.;
// list of reachRect
private transient Map<Shape, Basin> shapeBasinMap;
private transient Map<Basin, Shape> basinShapeMap;
// list of color
- //private transient Color[] colorList;
+ // private transient Color[] colorList;
@Override
public void init() {
- // create a uniform generator to calculate 100 xAlea and yAlea
+ // create a uniform generator to calculate 100 xAlea and yAlea
// to randomly locate the fish in a basin
nbAlea = 1000;
- aleaX=new double[nbAlea];
- aleaY=new double[nbAlea];
- for (int i=0; i < nbAlea; i++){
- aleaX[i]= Math.random();
- aleaY[i]= Math.random();
+ aleaX = new double[nbAlea];
+ aleaY = new double[nbAlea];
+ for (int i = 0; i < nbAlea; i++) {
+ aleaX[i] = Math.random();
+ aleaY[i] = Math.random();
}
display = new JPanel(new BorderLayout());
@@ -67,114 +65,96 @@ Drawable, MouseMotionListener {
display.add(displayComponent, BorderLayout.CENTER);
display.add(label, BorderLayout.PAGE_START);
- /* // color list
- colorList = new Color[6];
- colorList[0]= Color.GREEN;
- colorList[1]= Color.CYAN;
- colorList[2]= Color.MAGENTA;
- colorList[3]= Color.PINK;
- colorList[4]= Color.ORANGE;
- colorList[5]= Color.YELLOW;*/
-
-/* // list of color
- colors= new ArrayList<Color>(25);
- colors.add(new Color(0, 157, 0));
- colors.add(new Color(0, 163, 0));
- colors.add(new Color(0, 168, 0));
- colors.add(new Color(0, 172, 0));
- colors.add(new Color(17, 175, 0));
- colors.add(new Color(57, 178, 0));
- colors.add(new Color(82, 179, 0));
- colors.add(new Color(103, 180, 0));
- colors.add(new Color(122, 179, 0));
- colors.add(new Color(138, 178, 39));
- colors.add(new Color(153, 175, 117));
- colors.add(new Color(165, 173, 153));
- colors.add(new Color(171, 171, 171));
- colors.add(new Color(183, 167, 157));
- colors.add(new Color(201, 159, 127));
- colors.add(new Color(219, 149, 78));
- colors.add(new Color(235, 139, 0));
- colors.add(new Color(248, 127, 0));
- colors.add(new Color(255, 114, 0));
- colors.add(new Color(255, 101, 0));
- colors.add(new Color(255, 87, 0));
- colors.add(new Color(255, 72, 0));
- colors.add(new Color(255, 57, 0));
- colors.add(new Color(255, 39, 0));
- colors.add(new Color(255, 14, 0));*/
+ /*
+ * // color list colorList = new Color[6]; colorList[0]= Color.GREEN; colorList[1]= Color.CYAN; colorList[2]=
+ * Color.MAGENTA; colorList[3]= Color.PINK; colorList[4]= Color.ORANGE; colorList[5]= Color.YELLOW;
+ */
+
+ /*
+ * // list of color colors= new ArrayList<Color>(25); colors.add(new Color(0, 157, 0)); colors.add(new Color(0,
+ * 163, 0)); colors.add(new Color(0, 168, 0)); colors.add(new Color(0, 172, 0)); colors.add(new Color(17, 175,
+ * 0)); colors.add(new Color(57, 178, 0)); colors.add(new Color(82, 179, 0)); colors.add(new Color(103, 180,
+ * 0)); colors.add(new Color(122, 179, 0)); colors.add(new Color(138, 178, 39)); colors.add(new Color(153, 175,
+ * 117)); colors.add(new Color(165, 173, 153)); colors.add(new Color(171, 171, 171)); colors.add(new Color(183,
+ * 167, 157)); colors.add(new Color(201, 159, 127)); colors.add(new Color(219, 149, 78)); colors.add(new
+ * Color(235, 139, 0)); colors.add(new Color(248, 127, 0)); colors.add(new Color(255, 114, 0)); colors.add(new
+ * Color(255, 101, 0)); colors.add(new Color(255, 87, 0)); colors.add(new Color(255, 72, 0)); colors.add(new
+ * Color(255, 57, 0)); colors.add(new Color(255, 39, 0)); colors.add(new Color(255, 14, 0));
+ */
// list of color
- colors= new ArrayList<Color>(2);
+ colors = new ArrayList<Color>(2);
colors.add(Color.BLACK);
colors.add(Color.GRAY);
-
// Initialize the map linking shape with basin
shapeBasinMap = new HashMap<Shape, Basin>();
}
+
@Override
public JComponent getDisplay() {
// compute the range with a small margin
double marginRatio = .02;
- double surf= maxSurface/2, interRect=maxSurface*.05;
- minX = -2*(surf + interRect);
- rangeX = maxSurface - minX;
- minX -= rangeX *marginRatio;
- rangeX += 2*rangeX *marginRatio;
-
+ double surf = maxSurface / 2, interRect = maxSurface * .05;
+ minX = -2 * (surf + interRect);
+ rangeX = maxSurface - minX;
+ minX -= rangeX * marginRatio;
+ rangeX += 2 * rangeX * marginRatio;
+
bn = (GridBasinNetwork) pilot.getAquaticWorld().getEnvironment();
minY = Double.POSITIVE_INFINITY;
for (RiverBasin basin : bn.getRiverBasins()) {
- minY = Math.min(minY ,basin.getLatitude());
+ minY = Math.min(minY, basin.getLatitude());
}
- minY = (minY -minDistance/2.) ;
+ minY = (minY - minDistance / 2.);
rangeY = maxDistance - minY;
minY -= rangeY * marginRatio;
- rangeY += 2*rangeY*marginRatio;
+ rangeY += 2 * rangeY * marginRatio;
// define the shape for each basin
basinShapeMap = new HashMap<Basin, Shape>();
for (Basin basin : bn.getBasins()) {
Path2D.Double shape = new Path2D.Double();
- if (basin.getType() == BasinType.RIVER){
- shape.moveTo( 0., ((RiverBasin) basin).getLatitude()- minDistance/2);
- shape.lineTo(((RiverBasin) basin).getSurface(), ((RiverBasin) basin).getLatitude()- minDistance/2);
- shape.lineTo(((RiverBasin) basin).getSurface(), ((RiverBasin) basin).getLatitude()+ minDistance/2);
- shape.lineTo( 0., ((RiverBasin) basin).getLatitude()+ minDistance/2);
+ if (basin.getType() == BasinType.RIVER) {
+ shape.moveTo(0., ((RiverBasin) basin).getLatitude() - minDistance / 2);
+ shape.lineTo(((RiverBasin) basin).getSurface(), ((RiverBasin) basin).getLatitude() - minDistance / 2);
+ shape.lineTo(((RiverBasin) basin).getSurface(), ((RiverBasin) basin).getLatitude() + minDistance / 2);
+ shape.lineTo(0., ((RiverBasin) basin).getLatitude() + minDistance / 2);
shape.closePath();
} else {
RiverBasin rivBas = (RiverBasin) bn.getAssociatedRiverBasin(basin);
- double lag= surf +interRect;
+ double lag = surf + interRect;
if (basin.getType() == BasinType.OFFSHORE)
- lag *=2 ;
-
- shape.moveTo(-lag, rivBas.getLatitude()- minDistance/2);
- shape.lineTo(-lag+surf, rivBas.getLatitude()- minDistance/2);
- shape.lineTo( -lag+surf, rivBas.getLatitude()+ minDistance/2);
- shape.lineTo( -lag ,rivBas.getLatitude()+ minDistance/2);
+ lag *= 2;
+
+ shape.moveTo(-lag, rivBas.getLatitude() - minDistance / 2);
+ shape.lineTo(-lag + surf, rivBas.getLatitude() - minDistance / 2);
+ shape.lineTo(-lag + surf, rivBas.getLatitude() + minDistance / 2);
+ shape.lineTo(-lag, rivBas.getLatitude() + minDistance / 2);
shape.closePath();
}
basinShapeMap.put(basin, shape);
}
-
return display;
}
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new BasinNetworkObserverWith2Basins())); }
+
+
+ public static void main(String[] args) {
+ System.out.println((new XStream(new DomDriver())).toXML(new BasinNetworkObserverWith2Basins()));
+ }
private class DisplayComponent extends JComponent {
@Override
protected synchronized void paintComponent(Graphics g) {
- double W =this.getWidth();
- double H =this.getHeight();
- AffineTransform af = new AffineTransform(W/rangeX, 0., 0.,
- -H/rangeY, -W*minX/rangeX, H*(1. + minY/rangeY));
- //System.out.println(af.toString());
+ double W = this.getWidth();
+ double H = this.getHeight();
+ AffineTransform af = new AffineTransform(W / rangeX, 0., 0., -H / rangeY, -W * minX / rangeX,
+ H * (1. + minY / rangeY));
+ // System.out.println(af.toString());
// prepare the graphics
this.paintComponents(g);
@@ -187,23 +167,23 @@ Drawable, MouseMotionListener {
// prepare the diameter for the fish circle
double fishX, fishY;
- int fishDiameter = (int) Math.round(Math.min(W,H) / 100.);
+ int fishDiameter = (int) Math.round(Math.min(W, H) / 100.);
shapeBasinMap.clear();
int idxColor;
- //System.out.println("minX="+minX+ " rangeX=" + rangeX+ " minY="+minY+ "rangeY="+rangeY);
+ // System.out.println("minX="+minX+ " rangeX=" + rangeX+ " minY="+minY+ "rangeY="+rangeY);
for (Basin basin : basinShapeMap.keySet()) {
// draw each basin
- //System.out.println( basin.getName() +" "+ basinShapeMap.get(basin).getBounds2D().toString());
- Path2D.Double displayShape = (Path2D.Double)
- ((Path2D.Double) basinShapeMap.get(basin)).createTransformedShape(af);
- //System.out.println( basin.getName() +" "+ displayShape.getBounds2D().toString());
+ // System.out.println( basin.getName() +" "+ basinShapeMap.get(basin).getBounds2D().toString());
+ Path2D.Double displayShape = (Path2D.Double) ((Path2D.Double) basinShapeMap.get(basin))
+ .createTransformedShape(af);
+ // System.out.println( basin.getName() +" "+ displayShape.getBounds2D().toString());
shapeBasinMap.put(displayShape, basin); // to be used by the mouseMoved()
- // fill the
- if (basin instanceof RiverBasin)
+ // fill the
+ if (basin instanceof RiverBasin)
g.setColor(new Color(0, 204, 255));
else if (basin instanceof InshoreBasin)
g.setColor(new Color(0, 102, 255));
@@ -213,40 +193,35 @@ Drawable, MouseMotionListener {
g2d.fill(displayShape);
// draw the contour of the basin
- if (basin instanceof RiverBasin) {
+ if (basin instanceof RiverBasin) {
idxColor = bn.getRow(basin.getId()) % colors.size();
g.setColor(colors.get(idxColor));
g2d.draw(displayShape);
}
// draw fish
- int cpt=0;
- Map<DiadromousFishGroup, List<DiadromousFish>> fishPerGroup= basin.getFishPerGroup();
- for (DiadromousFishGroup group : fishPerGroup.keySet()){
- //g.setColor(group.getColor());
+ int cpt = 0;
+ Map<DiadromousFishGroup, List<DiadromousFish>> fishPerGroup = basin.getFishPerGroup();
+ for (DiadromousFishGroup group : fishPerGroup.keySet()) {
+ // g.setColor(group.getColor());
- for (DiadromousFish fish : fishPerGroup.get(group)){
+ for (DiadromousFish fish : fishPerGroup.get(group)) {
do {
- fishX = displayShape.getBounds2D().getMinX() + displayShape.getBounds2D().getWidth()
- * (0.2 + .6 * aleaX[cpt % nbAlea]); //- fishDiameter/2;
- fishY = displayShape.getBounds2D().getMinY()+ displayShape.getBounds2D().getHeight()
- * (0.2 + .6 * aleaY[cpt % nbAlea]);// - fishDiameter/2;
- //System.out.println(! displayShape.contains(fishX, fishY));
+ fishX = displayShape.getBounds2D().getMinX()
+ + displayShape.getBounds2D().getWidth() * (0.2 + .6 * aleaX[cpt % nbAlea]); // -
+ // fishDiameter/2;
+ fishY = displayShape.getBounds2D().getMinY()
+ + displayShape.getBounds2D().getHeight() * (0.2 + .6 * aleaY[cpt % nbAlea]);// -
+ // fishDiameter/2;
+ // System.out.println(! displayShape.contains(fishX, fishY));
cpt++;
- } while (! displayShape.contains(fishX, fishY));
+ } while (!displayShape.contains(fishX, fishY));
idxColor = bn.getRow(fish.getBirthBasin().getId()) % colors.size();
g.setColor(colors.get(idxColor));
- g2d.fillOval((int) fishX, (int) fishY, fishDiameter,
- fishDiameter);
+ g2d.fillOval((int) fishX, (int) fishY, fishDiameter, fishDiameter);
}
}
}
}
}
}
-
-
-
-
-
-
diff --git a/src/main/java/environment/BasinNetworkObserverWithRealBasin.java b/src/main/java/environment/BasinNetworkObserverWithRealBasin.java
index e338805b0282e9e0160f03138770b234646cffce..f0563a91883a57a1d342151d2350a21415f01c9b 100644
--- a/src/main/java/environment/BasinNetworkObserverWithRealBasin.java
+++ b/src/main/java/environment/BasinNetworkObserverWithRealBasin.java
@@ -33,9 +33,9 @@ import fr.cemagref.simaqualife.kernel.util.TransientParameters;
import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFishGroup;
+@Deprecated
@SuppressWarnings("serial")
-public class BasinNetworkObserverWithRealBasin extends ObserverListener
- implements Configurable, Drawable, MouseMotionListener {
+public class BasinNetworkObserverWithRealBasin extends ObserverListener implements Configurable, Drawable, MouseMotionListener {
private String title;
private double threshold = 13000000.;
@@ -131,8 +131,7 @@ public class BasinNetworkObserverWithRealBasin extends ObserverListener
txt += (basin.getName() + " ");
for (DiadromousFishGroup group : basin.getGroups()) {
- txt += group.getName() + "=" + basin.getEffective(group) + " in " + basin.getSuperFishNumber(group)
- + " SI ";
+ txt += group.getName() + "=" + basin.getEffective(group) + " in " + basin.getSuperFishNumber(group) + " SI ";
}
break;
}
diff --git a/src/main/java/environment/BasinNetworkReal.java b/src/main/java/environment/BasinNetworkReal.java
index 5c6654334e25544e72dde916714f046e9b7119e0..de76bd90f085b1e6ed8c2593834bea732241df3f 100644
--- a/src/main/java/environment/BasinNetworkReal.java
+++ b/src/main/java/environment/BasinNetworkReal.java
@@ -26,6 +26,7 @@ import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientPara
import fr.cemagref.simaqualife.pilot.Pilot;
import miscellaneous.QueueMemoryMap;
+@Deprecated
public class BasinNetworkReal extends GridBasinNetwork {
private String basinFile = "data/input/reality/basins.csv";
diff --git a/src/main/java/environment/BasinNetworkSWithContinent.java b/src/main/java/environment/BasinNetworkSWithContinent.java
index cd289c0077b4036b33a0e1afd17aeebc0d740d24..0427ac7e174e3b6a8f632698bcb4c5cacd1971f3 100644
--- a/src/main/java/environment/BasinNetworkSWithContinent.java
+++ b/src/main/java/environment/BasinNetworkSWithContinent.java
@@ -461,5 +461,4 @@ public class BasinNetworkSWithContinent extends GridBasinNetwork {
public Map<String, Path2D.Double> getMapContinent() {
return mapContinent;
}
-
}
diff --git a/src/main/java/environment/BasinNetworkWith2Basins.java b/src/main/java/environment/BasinNetworkWith2Basins.java
index 9646ca5ac24150aeac5b7b0d3b6d5d332b1b5299..5c7e360a95342ea406ee23e7a555398cdcea80f6 100644
--- a/src/main/java/environment/BasinNetworkWith2Basins.java
+++ b/src/main/java/environment/BasinNetworkWith2Basins.java
@@ -9,6 +9,7 @@ import environment.OffshoreBasin.OffshoreBasinFunction;
import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
import fr.cemagref.simaqualife.pilot.Pilot;
+@Deprecated
public class BasinNetworkWith2Basins extends GridBasinNetwork {
private String nameOfBv[] = { "BV1", "BV2" };
diff --git a/src/main/java/species/NutrientRoutineEssay.java b/src/main/java/species/NutrientRoutineEssay.java
index fe13c766c78b92d9d563327dffa346a98236617c..30e1ace17fa47e3ac1b1006e9267045a8796c460 100644
--- a/src/main/java/species/NutrientRoutineEssay.java
+++ b/src/main/java/species/NutrientRoutineEssay.java
@@ -1,10 +1,6 @@
package species;
-import environment.InshoreBasin;
-import fr.cemagref.simaqualife.pilot.Pilot;
-import species.DiadromousFish.Gender;
-import species.DiadromousFish.Stage;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Map;
@@ -12,188 +8,177 @@ import java.util.Map;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
+import environment.InshoreBasin;
+import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish.Gender;
+import species.DiadromousFish.Stage;
/**
* @author camille.poulet
*
*/
+@Deprecated
public class NutrientRoutineEssay {
+ private static enum SpawningPosition {
+ PRE, POST
+ }; // on cr�er un static pour r�server une m�me classe m�moire pour toutes les instances
- private static enum SpawningPosition {PRE,POST}; // on cr�er un static pour r�server une m�me classe m�moire pour toutes les instances
-
- //private static enum Gender {UNDIFFERENCIED, FEMALE, MALE};
+ // private static enum Gender {UNDIFFERENCIED, FEMALE, MALE};
private ArrayList<String> nutrientsOfInterest;
private double residenceTime;
- private Map<String, Double> excretionRate;
+ private Map<String, Double> excretionRate;
/**
- * Main feature for weight (g) computation before spawning i.e. gametes expelling according to gender, for a given length (cm)
- * //Voir pour un retour � la ligne lors du commentaire
- * key gender
- * value
- * key feature
- * value value
+ * Main feature for weight (g) computation before spawning i.e. gametes expelling according to gender, for a given
+ * length (cm) //Voir pour un retour � la ligne lors du commentaire key gender value key feature value value
*/
- private Map <DiadromousFish.Gender,Map<String, Double>> fishFeaturesPreSpawning;
+ private Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPreSpawning;
- private Map <DiadromousFish.Gender, Map<String, Double>> fishFeaturesPostSpawning;
+ private Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPostSpawning;
private Map<String, Double> juvenileFeatures;
-
/**
- * Weight of gametes spawned for both males and females
- * key gender
- * value g
- * usually computed as the difference between unspawned gonad (inbound) and spawned gonad (outbound; "spent gonad")
+ * Weight of gametes spawned for both males and females key gender value g usually computed as the difference
+ * between unspawned gonad (inbound) and spawned gonad (outbound; "spent gonad")
*/
- //private Map <DiadromousFish.Gender, Double> spawnedGametesWeight;
-
+ // private Map <DiadromousFish.Gender, Double> spawnedGametesWeight;
/**
- * chemical composition of carcass before gametes expelling (before spawning) i.e. soma + gonads + gametes
- * <key> gender
- * <value>
- * <key> chemical element
- * <value> value ratio element / (total wet weight) g/g
+ * chemical composition of carcass before gametes expelling (before spawning) i.e. soma + gonads + gametes <key>
+ * gender <value> <key> chemical element <value> value ratio element / (total wet weight) g/g
*/
- private Map<DiadromousFish.Gender,Map<String,Double>> compoCarcassPreSpawning;
-
- //package permettant la cr�ation d'une table de hachage ie fonctionnant en cl� -valeur. Cl� unique, mais valeur peut �tre associ�e � plusieurs cl�s;
- //La class d'objet Map a pour point faible la taille des donn�es � stocker. Plus on a de valeur dans la table, plus c'est lourd et lent! Donc, trouver un compromis entre temps de calcul et espace.
- //N'accepte pas la valeur nulle et thread safe i.e. utilisable simultan�ment par plusieurs �l�ments du programme.
+ private Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPreSpawning;
+ // package permettant la cr�ation d'une table de hachage ie fonctionnant en cl� -valeur. Cl� unique, mais valeur
+ // peut �tre associ�e � plusieurs cl�s;
+ // La class d'objet Map a pour point faible la taille des donn�es � stocker. Plus on a de valeur dans la table, plus
+ // c'est lourd et lent! Donc, trouver un compromis entre temps de calcul et espace.
+ // N'accepte pas la valeur nulle et thread safe i.e. utilisable simultan�ment par plusieurs �l�ments du programme.
/**
- * chemical composition of gametes estimated from the MIGADO dataset (BDalosesBruch)
- * <key> gender
- * <value>
- * <key> chemical element
- * <value> value
+ * chemical composition of gametes estimated from the MIGADO dataset (BDalosesBruch) <key> gender <value> <key>
+ * chemical element <value> value
*/
- private Map<DiadromousFish.Gender, Map<String,Double>> compoGametes;
+ private Map<DiadromousFish.Gender, Map<String, Double>> compoGametes;
// For juveniles - Based on Taverny (1991)
/**
- * chemical composition of juveniles
- * <key> chemical element
- * <value> value
+ * chemical composition of juveniles <key> chemical element <value> value
*/
- private Map<String,Double> compoJuvenile;
-
+ private Map<String, Double> compoJuvenile;
/**
- * Constructor based on the 5 Map of fish composition
+ * Constructor based on the 5 Map of fish composition
+ *
* @param fishFeaturesPreSpawning
* @param compoCarcassPreSpawning
* @param compoCarcassPostSpawning
* @param compoGametes
* @param compoJuvenile
*/
- public NutrientRoutineEssay(ArrayList<String> nutrientsOfInterest,
+ public NutrientRoutineEssay(ArrayList<String> nutrientsOfInterest,
- double residenceTime,
- Map <String, Double> excretionRate,
+ double residenceTime, Map<String, Double> excretionRate,
Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPreSpawning,
Map<DiadromousFish.Gender, Map<String, Double>> fishFeaturesPostSpawning,
Map<DiadromousFish.Gender, Map<String, Double>> compoCarcassPreSpawning,
- Map<DiadromousFish.Gender, Map<String, Double>> compoGametes,
- Map<String, Double> juvenileFeatures,
- Map<String, Double> compoJuvenile)
- {
+ Map<DiadromousFish.Gender, Map<String, Double>> compoGametes, Map<String, Double> juvenileFeatures,
+ Map<String, Double> compoJuvenile) {
super();
this.nutrientsOfInterest = nutrientsOfInterest;
- this.excretionRate = excretionRate;
- this.residenceTime = residenceTime;
+ this.excretionRate = excretionRate;
+ this.residenceTime = residenceTime;
this.fishFeaturesPreSpawning = fishFeaturesPreSpawning;
this.fishFeaturesPostSpawning = fishFeaturesPostSpawning;
this.compoCarcassPreSpawning = compoCarcassPreSpawning;
this.compoGametes = compoGametes;
this.juvenileFeatures = juvenileFeatures;
- this.compoJuvenile = compoJuvenile;
+ this.compoJuvenile = compoJuvenile;
}
+
/**
- * compute the nutrient fluxes for a single fish (in the super individual)
- * that dies before spawning
+ * compute the nutrient fluxes for a single fish (in the super individual) that dies before spawning
+ *
* @param fish
*/
- public Map<String,Double> computeNutrientsInputForDeadFish(DiadromousFish fish, ArrayList<String> nutrientsOfInterest) {
+ public Map<String, Double> computeNutrientsInputForDeadFish(DiadromousFish fish, ArrayList<String> nutrientsOfInterest) {
- Map<String,Double> nutrientsInput = new Hashtable<String, Double>(); // On cr�er ici une Map, classe m�re des hashtable (Homme = classe mere ie Map//Jules = hashtable)
+ Map<String, Double> nutrientsInput = new Hashtable<String, Double>(); // On cr�er ici une Map, classe m�re des
+ // hashtable (Homme = classe mere ie
+ // Map//Jules = hashtable)
for (String nutrient : nutrientsOfInterest) {
- if (fish.getStage()== Stage.MATURE) {
- double totalWeightPre = this.getWeight(fish,SpawningPosition.PRE);
- double carcass = totalWeightPre
- * compoCarcassPreSpawning.get(fish.getGender()).get(nutrient);
- double excretion = totalWeightPre
- * residenceTime
- * excretionRate.get(nutrient) ;
+ if (fish.getStage() == Stage.MATURE) {
+ double totalWeightPre = this.getWeight(fish, SpawningPosition.PRE);
+ double carcass = totalWeightPre * compoCarcassPreSpawning.get(fish.getGender()).get(nutrient);
+ double excretion = totalWeightPre * residenceTime * excretionRate.get(nutrient);
double nutrientImport = carcass + excretion;
- nutrientsInput.put(nutrient, nutrientImport);
- }
- else {
+ nutrientsInput.put(nutrient, nutrientImport);
+ } else {
nutrientsInput.put(nutrient, 0.);
}
}
- //TODO Multiply by fish amount
+ // TODO Multiply by fish amount
return nutrientsInput;
}
- public Map<String,Double> computeNutrientsInputForDeadFish(DiadromousFish fish) {
- return computeNutrientsInputForDeadFish(fish,this.nutrientsOfInterest);
+ public Map<String, Double> computeNutrientsInputForDeadFish(DiadromousFish fish) {
+
+ return computeNutrientsInputForDeadFish(fish, this.nutrientsOfInterest);
}
+
/**
- * compute the nutrient fluxes for a single fish (in the super individual)
- * that survives after spawning
- * Map: model output = element of interest ie string + double ie the quantification of this fluxes.
+ * compute the nutrient fluxes for a single fish (in the super individual) that survives after spawning Map: model
+ * output = element of interest ie string + double ie the quantification of this fluxes.
+ *
* @return nutrientsInput
*/
- public Map<String,Double>computeNutrientsInputForSurvivalAfterSpawning(DiadromousFish fish, ArrayList<String> nutrientsOfInterest) {
-
- Map<String,Double> nutrientsInput = new Hashtable<String,Double>();
- for (String nutrient: nutrientsOfInterest) {
- if (fish.getStage()==Stage.MATURE) {
- double totalWeightPre = this.getWeight(fish,SpawningPosition.PRE);
- double gametes = (this.getGonadWeight(fish, SpawningPosition.PRE) - this.getGonadWeight(fish, SpawningPosition.POST))
- * compoGametes.get(fish.getGender()).get(nutrient);
- double excretion = totalWeightPre
- * residenceTime
- * excretionRate.get(nutrient);
+ public Map<String, Double> computeNutrientsInputForSurvivalAfterSpawning(DiadromousFish fish,
+ ArrayList<String> nutrientsOfInterest) {
+
+ Map<String, Double> nutrientsInput = new Hashtable<String, Double>();
+ for (String nutrient : nutrientsOfInterest) {
+ if (fish.getStage() == Stage.MATURE) {
+ double totalWeightPre = this.getWeight(fish, SpawningPosition.PRE);
+ double gametes = (this.getGonadWeight(fish, SpawningPosition.PRE)
+ - this.getGonadWeight(fish, SpawningPosition.POST)) * compoGametes.get(fish.getGender()).get(nutrient);
+ double excretion = totalWeightPre * residenceTime * excretionRate.get(nutrient);
double nutrientImport = gametes + excretion;
- nutrientsInput.put(nutrient, nutrientImport);
- }
- else {
- nutrientsInput.put(nutrient,0.);
+ nutrientsInput.put(nutrient, nutrientImport);
+ } else {
+ nutrientsInput.put(nutrient, 0.);
}
}
return nutrientsInput;
- }
+ }
- public Map<String,Double>computeNutrientsInputForSurvivalAfterSpawning(DiadromousFish fish) {
+
+ public Map<String, Double> computeNutrientsInputForSurvivalAfterSpawning(DiadromousFish fish) {
return computeNutrientsInputForSurvivalAfterSpawning(fish, this.nutrientsOfInterest);
}
- public Map<String,Double> computeNutrientsExportForJuveniles(DiadromousFish juvenileFish, ArrayList<String>nutrientsOfInterest) {
- Map<String,Double> nutrientsExport = new Hashtable<String,Double>();
- for(String nutrient: nutrientsOfInterest) {
- if(juvenileFish.getStage()==Stage.IMMATURE) {
+ public Map<String, Double> computeNutrientsExportForJuveniles(DiadromousFish juvenileFish,
+ ArrayList<String> nutrientsOfInterest) {
+ Map<String, Double> nutrientsExport = new Hashtable<String, Double>();
+ for (String nutrient : nutrientsOfInterest) {
+ if (juvenileFish.getStage() == Stage.IMMATURE) {
double JuvenileMass = this.getWeight(juvenileFish);
nutrientsExport.put(nutrient, JuvenileMass * compoJuvenile.get(nutrient));
@@ -203,74 +188,83 @@ public class NutrientRoutineEssay {
return nutrientsExport;
}
- public Map<String,Double> computeNutrientsExportForJuveniles(DiadromousFish juvenileFish){
+
+ public Map<String, Double> computeNutrientsExportForJuveniles(DiadromousFish juvenileFish) {
return computeNutrientsExportForJuveniles(juvenileFish, this.nutrientsOfInterest);
}
+
/**
- * Compute the weight for a fish with length (cm)
+ * Compute the weight for a fish with length (cm)
+ *
* @param fish
* @return weight (g)
*/
- public double getWeight (DiadromousFish fish, SpawningPosition spawningPosition) {
-
- double weight = 0.;
- if (fish.getStage()==Stage.IMMATURE)
- weight = juvenileFeatures.get("aLW") * Math.pow(fish.getLength(),juvenileFeatures.get("bLW"));
- else //Stage.MATURE
- weight = fishFeaturesPreSpawning.get(fish.getGender()).get("aLW") * Math.pow(fish.getLength(), fishFeaturesPreSpawning.get(fish.getGender()).get("bLW") );
-
+ public double getWeight(DiadromousFish fish, SpawningPosition spawningPosition) {
+
+ double weight = 0.;
+ if (fish.getStage() == Stage.IMMATURE)
+ weight = juvenileFeatures.get("aLW") * Math.pow(fish.getLength(), juvenileFeatures.get("bLW"));
+ else // Stage.MATURE
+ weight = fishFeaturesPreSpawning.get(fish.getGender()).get("aLW")
+ * Math.pow(fish.getLength(), fishFeaturesPreSpawning.get(fish.getGender()).get("bLW"));
+
return weight;
}
+
/**
- * Compute the weight for a fish with length (cm)
+ * Compute the weight for a fish with length (cm)
+ *
* @param fish
* @return weight (g)
*/
- public double getWeight (DiadromousFish fish) {
+ public double getWeight(DiadromousFish fish) {
- return getWeight (fish, SpawningPosition.PRE);
+ return getWeight(fish, SpawningPosition.PRE);
}
/**
- * Compute the gonad weight for a fish with length (cm) to compute the gamete emission (g).
+ * Compute the gonad weight for a fish with length (cm) to compute the gamete emission (g).
+ *
* @param fish
* @return weight (g)
*/
- public double getGonadWeight (DiadromousFish fish, SpawningPosition spawningPosition) {
+ public double getGonadWeight(DiadromousFish fish, SpawningPosition spawningPosition) {
- double gonadWeight = 0.;
- if (fish.getStage()==Stage.MATURE);
- if (spawningPosition == SpawningPosition.PRE)
+ double gonadWeight = 0.;
+ if (fish.getStage() == Stage.MATURE)
+ ;
+ if (spawningPosition == SpawningPosition.PRE)
gonadWeight = Math.exp(fishFeaturesPreSpawning.get(fish.getGender()).get("aLW_Gonad")
- + fishFeaturesPreSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
- else
+ + fishFeaturesPreSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
+ else
gonadWeight = Math.exp(fishFeaturesPostSpawning.get(fish.getGender()).get("aLW_Gonad")
- + fishFeaturesPostSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
+ + fishFeaturesPostSpawning.get(fish.getGender()).get("bLW_Gonad") * Math.log(fish.getLength()));
return gonadWeight;
}
-
+
+
/**
- * Compute the gonad weight for a fish with length (cm) to compute the gamete emission (g).
+ * Compute the gonad weight for a fish with length (cm) to compute the gamete emission (g).
+ *
* @param fish
* @return weight (g)
*/
- public double getGonadWeight (DiadromousFish fish) {
-
- return getGonadWeight (fish, SpawningPosition.PRE);
- }
-
+ public double getGonadWeight(DiadromousFish fish) {
+ return getGonadWeight(fish, SpawningPosition.PRE);
+ }
public ArrayList<String> getNutrientsOfInterest() {
return nutrientsOfInterest;
}
+
/**
* @param args
*/
@@ -280,158 +274,177 @@ public class NutrientRoutineEssay {
/**
* @param args
*/
- public static void main(String[] args) {
+ public static void main(String[] args) {
-
- double aResidenceTime =30;
+ double aResidenceTime = 30;
System.out.println("aResidenceTime: " + aResidenceTime); //
-
- Map <String, Double> anExcretionRate = new Hashtable <String, Double>();
- anExcretionRate.put("N", 24.71E-6); //values from Barber et al, Alewifes in ug/g wet mass/hour : convertit en g
- anExcretionRate.put("P", 2.17E-6); //values from Barber et al, Alewifes in ug/g wet mass/hour: convertit en g
+ Map<String, Double> anExcretionRate = new Hashtable<String, Double>();
+ anExcretionRate.put("N", 24.71E-6); // values from Barber et al, Alewifes in ug/g wet mass/hour : convertit en g
+ anExcretionRate.put("P", 2.17E-6); // values from Barber et al, Alewifes in ug/g wet mass/hour: convertit en g
System.out.println("anExcretionRate: " + anExcretionRate.toString()); //
/*
- * A feature pre spawning
+ * A feature pre spawning
*/
- Map<Gender, Map<String, Double>> aFeaturePreSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
+ Map<Gender, Map<String, Double>> aFeaturePreSpawning = new Hashtable<DiadromousFish.Gender, Map<String, Double>>();
/*
* For females
*/
- Map<String,Double> aFeature = new Hashtable<String,Double>();
+ Map<String, Double> aFeature = new Hashtable<String, Double>();
- aFeature.put("bLW", 3.3429); //From Taverny
- aFeature.put("aLW", 1.2102E-6 * Math.pow(10., aFeature.get("bLW"))); //weight size relationship -- Conversion des g/mm en g.cm (from Taverny, 1991)
+ aFeature.put("bLW", 3.3429); // From Taverny
+ aFeature.put("aLW", 1.2102E-6 * Math.pow(10., aFeature.get("bLW"))); // weight size relationship -- Conversion
+ // des g/mm en g.cm (from Taverny, 1991)
aFeature.put("bLW_Gonad", 2.6729); // issu de la relation taille - poids des gonades Bruch
aFeature.put("aLW_Gonad", -5.2425); // issu de la relation taille - poids des gonades Bruch
-
+
aFeaturePreSpawning.put(Gender.FEMALE, aFeature);
/*
- * For males
+ * For males
*/
- aFeature = new Hashtable<String,Double>();
+ aFeature = new Hashtable<String, Double>();
aFeature.put("bLW", 3.2252);
- aFeature.put("aLW", 2.4386E-6 * Math.pow(10., aFeature.get("bLW"))); //weight size relationship from Taverny -- Conversion des g/mm en g.cm (from Taverny, 1991)
- aFeature.put("bLW_Gonad", 3.3838);
- aFeature.put("aLW_Gonad", -8.8744);
- aFeaturePreSpawning.put(Gender.MALE,aFeature);
+ aFeature.put("aLW", 2.4386E-6 * Math.pow(10., aFeature.get("bLW"))); // weight size relationship from Taverny --
+ // Conversion des g/mm en g.cm (from
+ // Taverny, 1991)
+ aFeature.put("bLW_Gonad", 3.3838);
+ aFeature.put("aLW_Gonad", -8.8744);
+ aFeaturePreSpawning.put(Gender.MALE, aFeature);
System.out.println("aFeaturePreSpawning: " + aFeaturePreSpawning.toString()); //
/*
- * a Feature post Spawning
+ * a Feature post Spawning
*/
- Map<Gender, Map<String, Double>> aFeaturePostSpawning = new Hashtable<DiadromousFish.Gender, Map<String,Double>>();
+ Map<Gender, Map<String, Double>> aFeaturePostSpawning = new Hashtable<DiadromousFish.Gender, Map<String, Double>>();
/*
- * For females
+ * For females
*/
- aFeature = new Hashtable<String,Double>();
-
+ aFeature = new Hashtable<String, Double>();
+
aFeature.put("aLW_Gonad", -6.6234); // issu de la relation taille - poids des gonades Bruch
aFeature.put("bLW_Gonad", 2.8545); // issu de la relation taille - poids des gonades Bruch
-
+
aFeaturePostSpawning.put(Gender.FEMALE, aFeature);
/*
- * For males
+ * For males
*/
- aFeature = new Hashtable<String,Double>();
+ aFeature = new Hashtable<String, Double>();
aFeature.put("aLW_Gonad", -11.285); // issu de la relation taille - poids des gonades Bruch
aFeature.put("bLW_Gonad", 3.8331); // issu de la relation taille - poids des gonades Bruch
-
- aFeaturePostSpawning.put(Gender.MALE,aFeature);
+
+ aFeaturePostSpawning.put(Gender.MALE, aFeature);
System.out.println("aFeaturePostSpawning: " + aFeaturePostSpawning.toString());
// carcass composition for fish before spawning
- Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
- Map<String,Double> aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 2.958 / 100.); //On remplit une collection avec un put. Values from Haskell (2018) Alosa sapidissima (%)
- aCompo.put("P", 0.673 / 100.); //Values from Haskell (2018) Alosa sapidissima (%)
- aCompoCarcassPreSpawning.put(Gender.FEMALE,aCompo);
-
- aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 2.941 / 100.); //Values from Haskell (2018) Alosa sapidissima (%)
+ Map<Gender, Map<String, Double>> aCompoCarcassPreSpawning = new Hashtable<DiadromousFish.Gender, Map<String, Double>>();
+ Map<String, Double> aCompo = new Hashtable<String, Double>();
+ aCompo.put("N", 2.958 / 100.); // On remplit une collection avec un put. Values from Haskell (2018) Alosa
+ // sapidissima (%)
+ aCompo.put("P", 0.673 / 100.); // Values from Haskell (2018) Alosa sapidissima (%)
+ aCompoCarcassPreSpawning.put(Gender.FEMALE, aCompo);
+
+ aCompo = new Hashtable<String, Double>();
+ aCompo.put("N", 2.941 / 100.); // Values from Haskell (2018) Alosa sapidissima (%)
aCompo.put("P", 0.666 / 100.);// Values from Haskell (2018) Alosa sapidissima (%)
- aCompoCarcassPreSpawning.put(Gender.MALE,aCompo);
+ aCompoCarcassPreSpawning.put(Gender.MALE, aCompo);
System.out.println("aCompoCarcassPreSpawning: " + aCompoCarcassPreSpawning.toString()); //
+ // Gametes composition approximated by the difference between gonads weight before and after spawning.
+ Map<Gender, Map<String, Double>> aCompoGametes = new Hashtable<DiadromousFish.Gender, Map<String, Double>>();
+ aCompo = new Hashtable<String, Double>();
+ aCompo.put("N", 3.242 / 100.); // On remplit une collection avec un put. From Haskel et al, 2018.
+ aCompo.put("P", 0.320 / 100.); // Haskel = %P, N, ici ratio donc divise par 100
+ aCompoGametes.put(Gender.FEMALE, aCompo);
- // Gametes composition approximated by the difference between gonads weight before and after spawning.
- Map<Gender, Map<String, Double>> aCompoGametes = new Hashtable<DiadromousFish.Gender,Map<String,Double>>();
- aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 3.242 / 100.); //On remplit une collection avec un put. From Haskel et al, 2018.
- aCompo.put("P", 0.320 / 100.); // Haskel = %P, N, ici ratio donc divise par 100
- aCompoGametes.put(Gender.FEMALE,aCompo);
-
- aCompo = new Hashtable<String,Double>();
- aCompo.put("N", 3.250 / 100.); // Approxim�e par la compo des gonades
+ aCompo = new Hashtable<String, Double>();
+ aCompo.put("N", 3.250 / 100.); // Approxim�e par la compo des gonades
aCompo.put("P", 0.724 / 100.);
- aCompoGametes.put(Gender.MALE,aCompo);
+ aCompoGametes.put(Gender.MALE, aCompo);
System.out.println("aCompoGametes:" + aCompoGametes.toString()); //
- // features for juveniles
+ // features for juveniles
- Map<String,Double> aJuvenileFeatures = new Hashtable<String, Double>();
- aJuvenileFeatures.put("bLW",3.0306);
- aJuvenileFeatures.put("aLW",Math.exp(-11.942) * Math.pow(10., aJuvenileFeatures.get("bLW")));
+ Map<String, Double> aJuvenileFeatures = new Hashtable<String, Double>();
+ aJuvenileFeatures.put("bLW", 3.0306);
+ aJuvenileFeatures.put("aLW", Math.exp(-11.942) * Math.pow(10., aJuvenileFeatures.get("bLW")));
- System.out.println("aJuvenileFeatures: " + aJuvenileFeatures.toString());
+ System.out.println("aJuvenileFeatures: " + aJuvenileFeatures.toString());
- // carcass composition for juveniles fish
- Map<String, Double> aCompoJuveniles = new Hashtable<String,Double>();
- aCompoJuveniles.put("N", 2.803 / 100.); //On remplit une collection avec un put. %N in wet weight (Haskell et al, 2017) on Alosa sapidissima
- aCompoJuveniles.put("P", 0.887 / 100.); //%P in wet weight (from Haskell et al, 2017) on Alosa sapidissima
+ // carcass composition for juveniles fish
+ Map<String, Double> aCompoJuveniles = new Hashtable<String, Double>();
+ aCompoJuveniles.put("N", 2.803 / 100.); // On remplit une collection avec un put. %N in wet weight (Haskell et
+ // al, 2017) on Alosa sapidissima
+ aCompoJuveniles.put("P", 0.887 / 100.); // %P in wet weight (from Haskell et al, 2017) on Alosa sapidissima
- System.out.println("aCompoJuveniles: " + aCompoJuveniles.toString());
+ System.out.println("aCompoJuveniles: " + aCompoJuveniles.toString());
- ArrayList <String> nutrientsOfInterest= new ArrayList <String>();
+ ArrayList<String> nutrientsOfInterest = new ArrayList<String>();
nutrientsOfInterest.add("N");
nutrientsOfInterest.add("P");
System.out.println("nutrientsOfInterest: " + nutrientsOfInterest);
-
- NutrientRoutineEssay fn = new NutrientRoutineEssay(nutrientsOfInterest,aResidenceTime, anExcretionRate, aFeaturePreSpawning, aFeaturePostSpawning,
- aCompoCarcassPreSpawning, aCompoGametes, aJuvenileFeatures, aCompoJuveniles);
-
- InshoreBasin basin = new InshoreBasin(0,"Bidon",10.,12., 14.,12.); //il faut aller dans "SeaBasin" dans "environement et regarder comment est construit le constructeur. Il lui faut ici un rang, un nom de bassin versant, et des temp�rature pour chaque saison
- Pilot pilot = new Pilot ();
- DiadromousFish fishFemale = new DiadromousFish (pilot, basin, 52., 1L, Gender.FEMALE); //Idem ici, on regarde comment est construit DiadromousFih et on lui donne les valeur de ce qu'il nous demande.
+ NutrientRoutineEssay fn = new NutrientRoutineEssay(nutrientsOfInterest, aResidenceTime, anExcretionRate,
+ aFeaturePreSpawning, aFeaturePostSpawning, aCompoCarcassPreSpawning, aCompoGametes, aJuvenileFeatures,
+ aCompoJuveniles);
+
+ InshoreBasin basin = new InshoreBasin(0, "Bidon", 10., 12., 14., 12.); // il faut aller dans "SeaBasin" dans
+ // "environement et regarder comment est
+ // construit le constructeur. Il lui
+ // faut ici un rang, un nom de bassin
+ // versant, et des temp�rature pour
+ // chaque saison
+ Pilot pilot = new Pilot();
+ DiadromousFish fishFemale = new DiadromousFish(pilot, basin, 52., 1L, Gender.FEMALE); // Idem ici, on regarde
+ // comment est construit
+ // DiadromousFih et on
+ // lui donne les valeur
+ // de ce qu'il nous
+ // demande.
fishFemale.setStage(Stage.MATURE);
- DiadromousFish fishMale = new DiadromousFish (pilot, basin, 47., 1L, Gender.MALE); //Idem ici, on regarde comment est construit DiadromousFih et on lui donne les valeur de ce qu'il nous demande.
+ DiadromousFish fishMale = new DiadromousFish(pilot, basin, 47., 1L, Gender.MALE); // Idem ici, on regarde
+ // comment est construit
+ // DiadromousFih et on lui
+ // donne les valeur de ce
+ // qu'il nous demande.
fishMale.setStage(Stage.MATURE);
- DiadromousFish juvenileFish = new DiadromousFish(pilot,basin,7.0,1L,Gender.UNDIFFERENCIED);
+ DiadromousFish juvenileFish = new DiadromousFish(pilot, basin, 7.0, 1L, Gender.UNDIFFERENCIED);
juvenileFish.setStage(Stage.IMMATURE);
- System.out.println(); // affiche une ligne blanche
- System.out.println(fishFemale.getGender() + ": " + fishFemale.getLength() + " cm " + fn.getWeight(fishFemale, SpawningPosition.PRE)+ " g " + fn.getWeight(fishFemale, SpawningPosition.POST));
+ System.out.println(); // affiche une ligne blanche
+ System.out.println(fishFemale.getGender() + ": " + fishFemale.getLength() + " cm "
+ + fn.getWeight(fishFemale, SpawningPosition.PRE) + " g " + fn.getWeight(fishFemale, SpawningPosition.POST));
System.out.println("\tNutrients Fluxes for dead fish " + fn.computeNutrientsInputForDeadFish(fishFemale).toString());
- System.out.println("\tNutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fishFemale).toString());
+ System.out.println(
+ "\tNutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fishFemale).toString());
- System.out.println(fishMale.getGender() + ": " + fishMale.getLength() + " cm " + fn.getWeight(fishMale, SpawningPosition.PRE)+ " g " + fn.getWeight(fishMale, SpawningPosition.POST));
+ System.out.println(fishMale.getGender() + ": " + fishMale.getLength() + " cm "
+ + fn.getWeight(fishMale, SpawningPosition.PRE) + " g " + fn.getWeight(fishMale, SpawningPosition.POST));
System.out.println("\tNutrients Fluxes for dead fish " + fn.computeNutrientsInputForDeadFish(fishMale).toString());
- System.out.println("\tNutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fishMale).toString());
+ System.out.println(
+ "\tNutrients Fluxes for survival " + fn.computeNutrientsInputForSurvivalAfterSpawning(fishMale).toString());
- System.out.println(juvenileFish.getStage() + ": " + juvenileFish.getLength() + " cm " + fn.getWeight(juvenileFish)+ " g ");
+ System.out
+ .println(juvenileFish.getStage() + ": " + juvenileFish.getLength() + " cm " + fn.getWeight(juvenileFish) + " g ");
System.out.println("\tNutrients Fluxes for juveniles " + fn.computeNutrientsExportForJuveniles(juvenileFish).toString());
-
- /* Create XML file
+ /*
+ * Create XML file
*
*/
- System.out.println((new XStream(new DomDriver())).toXML(fn));
+ System.out.println((new XStream(new DomDriver())).toXML(fn));
- }
+ }
}
-
-
diff --git a/src/main/java/species/WriteEffectiveAndBiomassImportFluxes.java b/src/main/java/species/WriteEffectiveAndBiomassImportFluxes.java
index be6b38b390765bec8d02dba297743b4f423ae5da..2146f10ef91ba70df240be83f9f09bd3a12e5303 100644
--- a/src/main/java/species/WriteEffectiveAndBiomassImportFluxes.java
+++ b/src/main/java/species/WriteEffectiveAndBiomassImportFluxes.java
@@ -39,7 +39,7 @@ import species.DiadromousFish.Stage;
/**
*
*/
-public class WriteEffectiveAndBiomassFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
+public class WriteEffectiveAndBiomassImportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
private Season exportSeason = Season.SPRING;
@@ -50,7 +50,7 @@ public class WriteEffectiveAndBiomassFluxes extends AquaNismsGroupProcess<Diadro
public static void main(String[] args) {
- System.out.println((new XStream(new DomDriver())).toXML(new WriteEffectiveAndBiomassFluxes()));
+ System.out.println((new XStream(new DomDriver())).toXML(new WriteEffectiveAndBiomassImportFluxes()));
}
diff --git a/src/main/java/species/WriteEffectivesFluxes.java b/src/main/java/species/WriteEffectivesFluxes.java
index c386fb2bd07e210c1d7a586f5d830b1d2902ef8f..51610858c9d94bd4861eae11fc9378bd066c4b32 100644
--- a/src/main/java/species/WriteEffectivesFluxes.java
+++ b/src/main/java/species/WriteEffectivesFluxes.java
@@ -39,6 +39,7 @@ import species.DiadromousFish.Stage;
/**
*
*/
+@Deprecated
public class WriteEffectivesFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
private Season exportSeason = Season.SPRING;
@@ -46,36 +47,42 @@ public class WriteEffectivesFluxes extends AquaNismsGroupProcess<DiadromousFish,
private String fileNameOutput = "effectiveFluxes";
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 WriteEffectivesFluxes()));
+ System.out.println((new XStream(new DomDriver())).toXML(new WriteEffectivesFluxes()));
}
- /* (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=";";
+ sep = ";";
}
+
@Override
public void doProcess(DiadromousFishGroup group) {
- if (bW==null){
- if (fileNameOutput != null){
- new File(group.getOutputPath()+fileNameOutput).getParentFile().mkdirs();
+ if (bW == null) {
+ 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");
@@ -85,40 +92,41 @@ public class WriteEffectivesFluxes extends AquaNismsGroupProcess<DiadromousFish,
}
}
-
try {
Time time = group.getEnvironment().getTime();
if (time.getSeason(pilot) == exportSeason & time.getYear(pilot) >= group.getMinYearToWrite()) {
for (RiverBasin migrationBasin : group.getEnvironment().getRiverBasins()) {
- //Create the map to get the abundance in each birth basin
- Map<String, Long> spawnerOriginsBeforeReproduction = new HashMap<String, Long>(group.getEnvironment().getRiverBasinNames().length);
- for (String basinName : group.getEnvironment().getRiverBasinNames()){
- spawnerOriginsBeforeReproduction.put(basinName, 0L);
+ // Create the map to get the abundance in each birth basin
+ Map<String, Long> spawnerOriginsBeforeReproduction = new HashMap<String, Long>(
+ group.getEnvironment().getRiverBasinNames().length);
+ for (String basinName : group.getEnvironment().getRiverBasinNames()) {
+ spawnerOriginsBeforeReproduction.put(basinName, 0L);
}
- //compute the cumulative effective per birth basin
+ // compute the cumulative effective per birth basin
if (migrationBasin.getFishs(group) != null) {
for (DiadromousFish fish : migrationBasin.getFishs(group)) {
if (fish.getStage() == Stage.MATURE) {
String birthBasinName = fish.getBirthBasin().getName();
- spawnerOriginsBeforeReproduction.put(birthBasinName, spawnerOriginsBeforeReproduction.get(birthBasinName) + fish.getAmount() );
+ spawnerOriginsBeforeReproduction.put(birthBasinName,
+ spawnerOriginsBeforeReproduction.get(birthBasinName) + fish.getAmount());
}
}
}
- //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(pilot) + 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+spawnerOriginsBeforeReproduction.get(birthBasinName));
+ bW.write(sep + spawnerOriginsBeforeReproduction.get(birthBasinName));
}
// 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();
}