Fix InputFactory ignore null.

Reviewed-on: #6

Projet.iml

@@ -4,6 +4,7 @@
     <exclude-output />
     <content url="file://$MODULE_DIR$">
       <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/tests" isTestSource="true" />
     </content>
     <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />

data/test.csv

@@ -1,4 +1,9 @@
 Sample_code;Station;Latitude;Longitude;Depth;d13C_raw;d13C_corr;d15N;C_N;StandardLength;TrophicLevel;Anisakis_abdominalcavity;Anisakis_Liver;Anisakis_gonads;Anisakis_stomach;NParasitesViscera;Anisakis_Muscle_Right;Anisakis_Muscle_Left;Aniskis_Muscle_total;NParasitesTotal
 TRACTRA_S0575_A0439;S0575;48.8692264;-4.3976635;96.84;-20.09735065;-19.14374028;12.52361179;4.316778148;257;3.117572211;7;1;0;1;9;1;3;4;13
 TRACTRA_S0575_A0440;S0575;48.8692264;-4.3976635;96.84;-20.02738845;-19.42703789;12.25444555;3.959950061;252;3.038405671;263;5;0;21;289;12;11;23;312
-TRACTRA_S0575_A0441;S0575;48.8692264;-4.3976635;96.84;-19.82735569;-18.83090708;12.97020596;4.360049101;254;3.248923438;51;1;12;1;65;2;3;5;70
+TRACTRA_S0575_A0441;S0575;48.8692264;-4.3976635;96.84;-19.82735569;-18.83090708;12.97020596;4.360049101;254;3.248923438;51;1;12;1;65;2;3;5;70
+TRACTRA_S0575_A0442;S0575;48.8692264;-4.3976635;96.84;-19.37802102;-18.26777864;13.43393806;4.4749923;242;3.385315231;158;6;0;1;165;9;19;28;193
+TRACTRA_S0575_A0443;S0575;48.8692264;-4.3976635;96.84;-18.20541518;-18.20541518;12.68793425;3.369189318;254;3.165902347;67;1;10;1;79;1;6;7;86
+TRACTRA_S0575_A0444;S0575;48.8692264;-4.3976635;96.84;-20.21559661;-18.91007641;12.62442312;4.672242625;251;3.147222601;140;1;0;0;141;3;6;9;150
+TRACTRA_S0575_A0888;S0575;48.8692264;-4.3976635;96.84;-20.21559661;-18.91007641;12.62442312;4.672242625;259;3.147222601;;;;;;;;;
+TRACTRA_S0575_A0445;S0575;48.8692264;-4.3976635;96.84;-19.43517323;-19.13886211;11.25439721;3.65283952;258;2.744273805;281;5;0;3;289;1;8;9;298

src/ecoparasite/completion/Completion.java

@@ -0,0 +1,35 @@
+package ecoparasite.completion;
+
+import ecoparasite.poisson.Poisson;
+
+import java.util.HashSet;
+
+public class Completion {
+
+    public static HashSet<Poisson> completePoisson(HashSet<Poisson> tablePoisson){
+
+        double mean = mean(tablePoisson);
+
+        for (Poisson p : tablePoisson) {
+
+            if ( p.getInfestation().isNaN() ) {
+                p.setInfestation(mean);
+            }
+        }
+
+        return tablePoisson;
+    }
+
+    private static double mean(HashSet<Poisson> tablePoisson){
+
+        double mean = 0.0;
+
+        for (Poisson p : tablePoisson){
+            mean += p.getInfestation();
+        }
+
+        return mean / tablePoisson.size();
+    }
+
+
+}

src/ecoparasite/input/InputFactory.java

@@ -2,11 +2,13 @@ package ecoparasite.input;
 
 import java.io.BufferedReader;
 import java.io.IOException;
+import java.lang.reflect.Array;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 
 /**
@@ -93,7 +95,7 @@ public class InputFactory {
         // Lecture des autres lignes.
         try {
             while ((line = reader.readLine()) != null) {
-                rowFields = line.split(separator);
+                rowFields = line.split(separator, -1);
                 for (int i = 0; i < rowFields.length; i++) {
                     ArrayList<String> element = data.get(i);
                     element.add(rowFields[i]);

src/ecoparasite/nettoyage/Nettoyage.java

@@ -0,0 +1,63 @@
+package ecoparasite.nettoyage;
+
+import ecoparasite.poisson.Poisson;
+
+import java.util.HashSet;
+
+public class Nettoyage {
+
+    /**
+     *
+     * @param tablePoisson
+     * @return
+     */
+    public static HashSet<Poisson> nettoiePoisson(HashSet<Poisson> tablePoisson){
+
+        double mean = mean(tablePoisson); //Moyenne
+        double ecart = ecartType(tablePoisson); // Ecart Type
+
+        double z = 0;
+
+        for (Poisson p : tablePoisson) {
+            z = ( p.getInfestation() - mean ) / ecart;
+
+            if ( z >= 3 ) {
+                p.setInfestation(mean);
+            }
+        }
+
+        return tablePoisson;
+    }
+
+    private static double mean(HashSet<Poisson> tablePoisson){
+
+        double mean = 0.0;
+
+        for (Poisson p : tablePoisson){
+            mean += p.getInfestation();
+        }
+
+        return mean / tablePoisson.size();
+    }
+
+    private static double variance(HashSet<Poisson> tablePoisson){
+
+        double vari = 0.0;
+        double mean = mean(tablePoisson);
+
+        for (Poisson p : tablePoisson) {
+            vari += Math.pow( (p.getInfestation() - mean), 2);
+        }
+
+        return vari / tablePoisson.size();
+    }
+
+    private static double ecartType(HashSet<Poisson> tablePoisson){
+
+        double vari = variance(tablePoisson);
+
+        return Math.sqrt(vari);
+    }
+
+
+}

src/ecoparasite/poisson/Poisson.java

@@ -69,6 +69,15 @@ public class Poisson{
         return fishParts;
     }
 
+    /**
+     * Setter de l'attribut infestation
+     * @param infestation le Double de la nouvelle valeur de l'infestation
+     */
+    public void setInfestation(Double infestation) {
+        this.infestation = infestation;
+    }
+
+
     /**
      * Setter de l'attribut des parties de poisson.
      * @param fishParts Un hashset de parties de poisson.

tests/ecoparasite/completion/CompletionTest.java

@@ -0,0 +1,28 @@
+package ecoparasite.completion;
+
+import ecoparasite.input.InputFactory;
+import ecoparasite.input.InputFileException;
+import ecoparasite.input.RawData;
+import ecoparasite.input.RawDataOverflow;
+import ecoparasite.poisson.Mackerel;
+import ecoparasite.poisson.Poisson;
+import org.junit.jupiter.api.Test;
+
+import java.util.HashSet;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class CompletionTest {
+
+    @org.junit.jupiter.api.Test
+    void completePoisson() throws InputFileException, RawDataOverflow {
+
+        RawData test = InputFactory.readData("test.csv");
+
+        HashSet<Poisson> testp = Mackerel.parse(test);
+
+        testp = Completion.completePoisson(testp);
+
+        System.out.println(testp);
+    }
+}