add comments

src/main/java/GraphModificationFunctions.java

@@ -8,7 +8,7 @@ import java.util.Map;
 
 public interface GraphModificationFunctions {
 
-    //remove over- and under-weight edges
+    //remove over- and under-weight edges, return removed edges
     static Map<Vertex[], Integer> filterByOverlapThresholds(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
                                                             int low, int high, boolean saveEdges) {
         Map<Vertex[], Integer> removedEdges = new HashMap<>();
@@ -35,7 +35,7 @@ public interface GraphModificationFunctions {
         return removedEdges;
     }
 
-    //Remove edges for pairs with large occupancy discrepancy
+    //Remove edges for pairs with large occupancy discrepancy, return removed edges
     static Map<Vertex[], Integer> filterByRelativeOccupancy(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
                                                   Integer maxOccupancyDifference, boolean saveEdges) {
         Map<Vertex[], Integer> removedEdges = new HashMap<>();
@@ -63,7 +63,7 @@ public interface GraphModificationFunctions {
         return removedEdges;
     }
 
-    //Remove edges for pairs where overlap size is significantly lower than the well occupancy
+    //Remove edges for pairs where overlap size is significantly lower than the well occupancy, return removed edges
     static Map<Vertex[], Integer> filterByOverlapPercent(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
                                                          Integer minOverlapPercent,
                                                          boolean saveEdges) {

src/main/java/Simulator.java

@@ -47,7 +47,7 @@ public class Simulator implements GraphModificationFunctions {
         if(verbose){System.out.println("All betas count: " + betaCount);}
         if(verbose){System.out.println("Well maps made");}
 
-
+        //ideally we wouldn't do any graph pre-filtering. But sequences present in all wells add a huge number of edges to the graph and don't carry any signal value
         if(verbose){System.out.println("Removing sequences present in all wells.");}
         filterByOccupancyThresholds(allAlphas, 1, numWells - 1);
         filterByOccupancyThresholds(allBetas, 1, numWells - 1);
@@ -105,7 +105,9 @@ public class Simulator implements GraphModificationFunctions {
             Vertex alphaVertex = new Vertex(SequenceType.CDR3_ALPHA, seq, alphaWellCounts.get(seq), plateAtoVMap.get(seq));
             alphaVertices.add(alphaVertex);
         }
+        //Sort to make sure the order of vertices in list matches the order of the adjacency matrix
         Collections.sort(alphaVertices);
+        //Add ordered list of vertices to the graph
         graphGenerator.first(alphaVertices);
         //the list of beta vertices
         //List<Integer> betaVertices = new ArrayList<>(plateVtoBMap.keySet());//This will work because LinkedHashMap preserves order of entry
@@ -114,7 +116,9 @@ public class Simulator implements GraphModificationFunctions {
             Vertex betaVertex = new Vertex(SequenceType.CDR3_BETA, seq, betaWellCounts.get(seq), plateBtoVMap.get(seq));
             betaVertices.add(betaVertex);
         }
+        //Sort to make sure the order of vertices in list matches the order of the adjacency matrix
         Collections.sort(betaVertices);
+        //Add ordered list of vertices to the graph
         graphGenerator.second(betaVertices);
         //use adjacency matrix of weight created previously
         graphGenerator.weights(weights);