Add dropout rate calculation to read-in of data from plate file (this may slow down read-in by a lot)

src/main/java/Plate.java

@@ -61,12 +61,25 @@ public class Plate {
         this.wells = wells;
         this.size = wells.size();
 
+        double totalCellCount = 0.0;
+        double totalDropoutCount = 0.0;
         List<Integer> concentrations = new ArrayList<>();
         for (List<String[]> w: wells) {
+            totalCellCount += w.size();
             if(!concentrations.contains(w.size())){
                 concentrations.add(w.size());
             }
+            for (String[] cell: w) {
+                totalCellCount += 1.0;
+                for (String sequence: cell) {
+                    if("-1".equals(sequence)) {
+                        totalDropoutCount += 1.0;
+                    }
+                }
+            }
         }
+        double totalSequenceCount = totalCellCount * 4;
+        this.error = totalDropoutCount / totalSequenceCount;
         this.populations = new Integer[concentrations.size()];
         for (int i = 0; i < this.populations.length; i++) {
             this.populations[i] = concentrations.get(i);