Command line arguments working, need better documentation and error handling

src/main/java/Plate.java

@@ -1,6 +1,7 @@
 import java.util.*;
 
 /*
+TODO: Implement exponential distribution using inversion method - DONE
 TODO: Implement discrete frequency distributions using Vose's Alias Method
  */
 
@@ -12,13 +13,15 @@ public class Plate {
     private double error;
     private Integer[] concentrations;
     private double stdDev;
+    private double lambda;
+    boolean exponential = false;
 
 
-    public Plate (int size, double error, Integer[] concentrations, double stdDev) {
+    public Plate (int size, double error, Integer[] concentrations) {
         this.size = size;
         this.error = error;
         this.concentrations = concentrations;
-        this.stdDev = stdDev;
+        //this.stdDev = stdDev;
         wells = new ArrayList<>();
     }
 
@@ -28,7 +31,47 @@ public class Plate {
         this.size = wells.size();
     }
 
-    public void fillWells(String sourceFileName, List<Integer[]> cells) {
+    public void fillWellsExponential(String sourceFileName, List<Integer[]> cells, double lambda){
+        this.lambda = lambda;
+        exponential = true;
+        sourceFile = sourceFileName;
+        int numSections = concentrations.length;
+        int section = 0;
+        double m;
+        int n;
+        int test=0;
+        while (section < numSections){
+            for (int i = 0; i < (size / numSections); i++) {
+                List<Integer[]> well = new ArrayList<>();
+                for (int j = 0; j < concentrations[section]; j++) {
+                    do {
+                        m = (Math.log10((1 - rand.nextDouble()))/(-lambda)) * Math.sqrt(cells.size());
+                    } while (m >= cells.size() || m < 0);
+                    n = (int) Math.floor(m);
+                    //n = Equations.getRandomNumber(0, cells.size());
+                    // was testing generating the cell sample file with exponential dist, then sampling flat here
+                    //that would be more realistic
+                    //But would mess up my
+                    if(n > test){
+                        test = n;
+                    }
+                    Integer[] cellToAdd = cells.get(n).clone();
+                    for(int k = 0; k < cellToAdd.length; k++){
+                        if(Math.abs(rand.nextDouble()) < error){//error applied to each peptide
+                            cellToAdd[k] = -1;
+                        }
+                    }
+                    well.add(cellToAdd);
+                }
+                wells.add(well);
+            }
+            section++;
+        }
+        System.out.println("Highest index: " +test);
+    }
+
+    public void fillWells(String sourceFileName, List<Integer[]> cells, double stdDev) {
+        this.stdDev = stdDev;
         sourceFile = sourceFileName;
         int numSections = concentrations.length;
         int section = 0;
@@ -68,6 +111,10 @@ public class Plate {
         return stdDev;
     }
 
+    public boolean isExponential(){return exponential;}
+
+    public double getLambda(){return lambda;}
+
     public double getError() {
         return error;
     }