Do new filtering before matching

src/main/java/Simulator.java

@@ -194,6 +194,16 @@ public class Simulator {
         filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
         if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
 
+        //Filter by overlap size
+        if(verbose){System.out.println("Eliminating edges with weights much less than occupancy values");}
+        filterByOverlapSize(graph, alphaWellCounts, betaWellCounts);
+        if(verbose){System.out.println("Edges with weights much less than occupancy values set to 0.0");}
+
+        //Filter by relative occupancy
+        if(verbose){System.out.println("Eliminating edges between vertices of massively different occupancy");}
+        filterByRelativeOccupancy(graph, alphaWellCounts, betaWellCounts);
+        if(verbose){System.out.println("Edges between vertices of massively different occupancy set to 0.0");}
+
 
         /**
          * This is where the maximum weighted matching is found
@@ -666,6 +676,35 @@ public class Simulator {
         }
     }
 
+    //Remove edges for pairs with large occupancy discrepancy
+    private static void filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                                  Map<Integer, Integer> alphaWellCounts,
+                                                  Map<Integer, Integer> betaWellCounts) {
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            Integer alphaOcc = alphaWellCounts.get(graph.getEdgeSource(e));
+            Integer betaOcc = betaWellCounts.get(graph.getEdgeTarget(e));
+            //Adjust this to something cleverer later
+            if (Math.abs(alphaOcc - betaOcc) >= 20) {
+                graph.setEdgeWeight(e, 0.0);
+            }
+        }
+    }
+
+    //Remove edges for pairs where overlap size is significantly lower than the well occupancy
+    private static void filterByOverlapSize(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
+                                            Map<Integer, Integer> alphaWellCounts,
+                                            Map<Integer, Integer> betaWellCounts) {
+        for (DefaultWeightedEdge e : graph.edgeSet()) {
+            Integer alphaOcc = alphaWellCounts.get(graph.getEdgeSource(e));
+            Integer betaOcc = betaWellCounts.get(graph.getEdgeTarget(e));
+            //Adjust this to something cleverer later
+            Integer min = alphaOcc > betaOcc ? betaOcc : alphaOcc;
+            if (min - graph.getEdgeWeight(e) >= 15) {
+                graph.setEdgeWeight(e, 0.0);
+            }
+        }
+    }
+
     private static Map<Integer, Integer> makePeptideToPeptideMap(List<Integer[]> cells, int keyPeptideIndex,
                                                                  int valuePeptideIndex){
         Map<Integer, Integer> keyPeptideToValuePeptideMap = new HashMap<>();
@@ -693,9 +732,4 @@ public class Simulator {
         return inverse;
     }
 
-    private static int bigDecimalComparator(BigDecimal bd, Integer i) {
-        return bd.compareTo(BigDecimal.valueOf(i));
-    }
-
-
 }