Added metadata to MatchingResult to enable CLI options

src/main/java/Plate.java

@@ -1,26 +1,28 @@
-import java.util.*;
+
 
 /*
 TODO: Implement exponential distribution using inversion method - DONE
 TODO: Implement discrete frequency distributions using Vose's Alias Method
  */
 
+import java.util.*;
+
 public class Plate {
     private String sourceFile;
     private List<List<Integer[]>> wells;
     private Random rand = new Random();
     private int size;
     private double error;
-    private Integer[] concentrations;
+    private Integer[] populations;
     private double stdDev;
     private double lambda;
     boolean exponential = false;
 
 
-    public Plate(int size, double error, Integer[] concentrations) {
+    public Plate(int size, double error, Integer[] populations) {
         this.size = size;
         this.error = error;
-        this.concentrations = concentrations;
+        this.populations = populations;
         wells = new ArrayList<>();
     }
 
@@ -35,9 +37,9 @@ public class Plate {
                 concentrations.add(w.size());
             }
         }
-        this.concentrations = new Integer[concentrations.size()];
-        for (int i = 0; i < this.concentrations.length; i++) {
-            this.concentrations[i] = concentrations.get(i);
+        this.populations = new Integer[concentrations.size()];
+        for (int i = 0; i < this.populations.length; i++) {
+            this.populations[i] = concentrations.get(i);
         }
     }
 
@@ -45,7 +47,7 @@ public class Plate {
         this.lambda = lambda;
         exponential = true;
         sourceFile = sourceFileName;
-        int numSections = concentrations.length;
+        int numSections = populations.length;
         int section = 0;
         double m;
         int n;
@@ -53,7 +55,7 @@ public class Plate {
         while (section < numSections){
             for (int i = 0; i < (size / numSections); i++) {
                 List<Integer[]> well = new ArrayList<>();
-                for (int j = 0; j < concentrations[section]; j++) {
+                for (int j = 0; j < populations[section]; j++) {
                     do {
                         //inverse transform sampling: for random number u in [0,1), x = log(1-u) / (-lambda)
                         m = (Math.log10((1 - rand.nextDouble()))/(-lambda)) * Math.sqrt(cells.size());
@@ -84,14 +86,14 @@ public class Plate {
     public void fillWells(String sourceFileName, List<Integer[]> cells, double stdDev) {
         this.stdDev = stdDev;
         sourceFile = sourceFileName;
-        int numSections = concentrations.length;
+        int numSections = populations.length;
         int section = 0;
         double m;
         int n;
         while (section < numSections){
             for (int i = 0; i < (size / numSections); i++) {
                 List<Integer[]> well = new ArrayList<>();
-                for (int j = 0; j < concentrations[section]; j++) {
+                for (int j = 0; j < populations[section]; j++) {
                     do {
                         m = (rand.nextGaussian() * stdDev) + (cells.size() / 2);
                     } while (m >= cells.size() || m < 0);
@@ -110,8 +112,8 @@ public class Plate {
         }
     }
 
-    public Integer[] getConcentrations(){
-        return concentrations;
+    public Integer[] getPopulations(){
+        return populations;
     }
 
     public int getSize(){