Sort vertex lists by vertex label before making adjacency matrix

src/main/java/Simulator.java

@@ -105,6 +105,7 @@ public class Simulator implements GraphModificationFunctions {
             Vertex alphaVertex = new Vertex(SequenceType.CDR3_ALPHA, seq, alphaWellCounts.get(seq), plateAtoVMap.get(seq));
             alphaVertices.add(alphaVertex);
         }
+        Collections.sort(alphaVertices);
         graphGenerator.first(alphaVertices);
         //the list of beta vertices
         //List<Integer> betaVertices = new ArrayList<>(plateVtoBMap.keySet());//This will work because LinkedHashMap preserves order of entry
@@ -113,6 +114,7 @@ public class Simulator implements GraphModificationFunctions {
             Vertex betaVertex = new Vertex(SequenceType.CDR3_BETA, seq, betaWellCounts.get(seq), plateBtoVMap.get(seq));
             betaVertices.add(betaVertex);
         }
+        Collections.sort(betaVertices);
         graphGenerator.second(betaVertices);
         //use adjacency matrix of weight created previously
         graphGenerator.weights(weights);

src/main/java/Vertex.java

@@ -1,6 +1,6 @@
 import java.io.Serializable;
 
-public class Vertex implements Serializable {
+public class Vertex implements Serializable, Comparable<Vertex> {
     private  SequenceType type;
     private  Integer vertexLabel;
     private  Integer sequence;
@@ -89,4 +89,9 @@ public class Vertex implements Serializable {
         return sb.toString();
     }
 
+    @Override
+    public int compareTo(Vertex other) {
+        return this.vertexLabel - other.getVertexLabel();
+    }
+
 }