Changing graph to use Vertex class

src/main/java/CellSample.java

@@ -13,8 +13,12 @@ public class CellSample {
         List<Integer> numbersCDR3 = new ArrayList<>();
         List<Integer> numbersCDR1 = new ArrayList<>();
         Integer numDistCDR3s = 2 * numDistinctCells + 1;
+        //Assign consecutive integers for each CDR3. This ensures they are all unique.
         IntStream.range(1, numDistCDR3s + 1).forEach(i -> numbersCDR3.add(i));
+        //After all CDR3s are assigned, start assigning consecutive integers to CDR1s
+        //There will usually be fewer integers in the CDR1 list, which will allow repeats below
         IntStream.range(numDistCDR3s + 1, numDistCDR3s + 1 + (numDistCDR3s / cdr1Freq) + 1).forEach(i -> numbersCDR1.add(i));
+        //randomize the order of the numbers in the lists
         Collections.shuffle(numbersCDR3);
         Collections.shuffle(numbersCDR1);
 
@@ -22,11 +26,15 @@ public class CellSample {
         //two CDR3s, and two CDR1s. First two values are CDR3s (alpha, beta), second two are CDR1s (alpha, beta)
         List<Integer[]> distinctCells = new ArrayList<>();
         for(int i = 0; i < numbersCDR3.size() - 1; i = i + 2){
+            //Go through entire CDR3 list once, make pairs of alphas and betas
             Integer tmpCDR3a = numbersCDR3.get(i);
             Integer tmpCDR3b = numbersCDR3.get(i+1);
+            //Go through (likely shorter) CDR1 list as many times as necessary, make pairs of alphas and betas
             Integer tmpCDR1a = numbersCDR1.get(i % numbersCDR1.size());
             Integer tmpCDR1b = numbersCDR1.get((i+1) % numbersCDR1.size());
+            //Make the array representing the cell
             Integer[] tmp = {tmpCDR3a, tmpCDR3b, tmpCDR1a, tmpCDR1b};
+            //Add the cell to the list of distinct cells
             distinctCells.add(tmp);
         }
         this.cells = distinctCells;