iterate over vertex wells correctly

src/main/java/Simulator.java

@@ -148,17 +148,23 @@ public class Simulator implements GraphModificationFunctions {
         }
         betaVertices.forEach(graph::addVertex);
         //add edges
-        for(Vertex alpha: alphaVertices){
-            for(Vertex beta: betaVertices) {
-                Set<Integer> sharedWells = alpha.getRecord().getWells();
-                sharedWells.retainAll(beta.getRecord().getWells());
-                if(!sharedWells.isEmpty()) {
-                    DefaultWeightedEdge edge = graph.addEdge(alpha, beta);
-                    graph.setEdgeWeight(edge, sharedWells.size());
+        for(Vertex a: alphaVertices) {
+            for(Integer well: a.getRecord().getWells()) {
+                for (Vertex b: betaVertices) {
+                    if (b.getRecord().isInWell(well)) {
+                        DefaultWeightedEdge edge = graph.getEdge(a, b);
+                        if (edge == null) {
+                            edge = graph.addEdge(a, b);
+                            graph.setEdgeWeight(edge, 1.0);
+                        }
+                        else {
+                            double weight = graph.getEdgeWeight(edge);
+                            graph.setEdgeWeight(edge, weight + 1.0);
+                        }
+                    }
                 }
             }
         }
-
         if(verbose){System.out.println("Graph created");}
         //stop timing
         Instant stop = Instant.now();