Correct propogation of peptide counts

src/main/java/GraphWithMapData.java

@@ -11,11 +11,11 @@ public class GraphWithMapData implements java.io.Serializable {
     private String sourceFilename;
     private final SimpleWeightedGraph graph;
     private Integer numWells;
+    private Integer alphaCount;
+    private Integer betaCount;
     private Integer lowThreshold;
     private Integer highThreshold;
     private final Map<Integer, Integer> distCellsMapAlphaKey;
-    private final Map<Integer, Integer> allAlphas;
-    private final Map<Integer, Integer> allBetas;
     private final Map<Integer, Integer> plateVtoAMap;
     private final Map<Integer, Integer> plateVtoBMap;
     private final Map<Integer, Integer> plateAtoVMap;
@@ -24,19 +24,19 @@ public class GraphWithMapData implements java.io.Serializable {
     private final Map<Integer, Integer> betaWellCounts;
     private final Duration time;
 
-    public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer lowThreshold, Integer highThreshold,
+    public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer alphaCount, Integer betaCount,
-                            Map<Integer, Integer> distCellsMapAlphaKey, Map<Integer, Integer> allAlphas,
+                            Integer lowThreshold, Integer highThreshold,
-                            Map<Integer, Integer> allBetas, Map<Integer, Integer> plateVtoAMap,
+                            Map<Integer, Integer> distCellsMapAlphaKey, Map<Integer, Integer> plateVtoAMap,
                             Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
                             Map<Integer, Integer> plateBtoVMap, Map<Integer, Integer> alphaWellCounts,
                             Map<Integer, Integer> betaWellCounts, Duration time) {
         this.graph = graph;
         this.numWells = numWells;
+        this.alphaCount = alphaCount;
+        this.betaCount = betaCount;
         this.lowThreshold = lowThreshold;
         this.highThreshold = highThreshold;
         this.distCellsMapAlphaKey = distCellsMapAlphaKey;
-        this.allAlphas = allAlphas;
-        this.allBetas = allBetas;
         this.plateVtoAMap = plateVtoAMap;
         this.plateVtoBMap = plateVtoBMap;
         this.plateAtoVMap = plateAtoVMap;
@@ -54,6 +54,14 @@ public class GraphWithMapData implements java.io.Serializable {
         return numWells;
     }
 
+    public Integer getAlphaCount() {
+        return alphaCount;
+    }
+
+    public Integer getBetaCount() {
+        return betaCount;
+    }
+
     public Integer getLowThreshold() {
         return lowThreshold;
     }
@@ -66,14 +74,6 @@ public class GraphWithMapData implements java.io.Serializable {
         return distCellsMapAlphaKey;
     }
 
-    public Map<Integer, Integer> getAllAlphas() {
-        return allAlphas;
-    }
-
-    public Map<Integer, Integer> getAllBetas() {
-        return allBetas;
-    }
-
     public Map<Integer, Integer> getPlateVtoAMap() {
         return plateVtoAMap;
     }

src/main/java/Simulator.java

@@ -142,9 +142,9 @@ public class Simulator {
         if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
         Instant stop = Instant.now();
         Duration time = Duration.between(start, stop);
-        return new GraphWithMapData(graph, numWells, lowThreshold, highThreshold, distCellsMapAlphaKey, allAlphas,
+        return new GraphWithMapData(graph, numWells, alphaCount, betaCount, lowThreshold, highThreshold,
-                allBetas, plateVtoAMap, plateVtoBMap, plateAtoVMap, plateBtoVMap, alphaWellCounts, betaWellCounts,
+                distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap, plateAtoVMap,
-                time);
+                plateBtoVMap, alphaWellCounts, betaWellCounts, time);
     }
 
     //match CDR3s
@@ -154,15 +154,13 @@ public class Simulator {
         int numWells = data.getNumWells();
         Integer highThreshold = data.getHighThreshold();
         Integer lowThreshold = data.getLowThreshold();
+        Integer alphaCount = data.getAlphaCount();
+        Integer betaCount = data.getBetaCount();
         Map<Integer, Integer> distCellsMapAlphaKey = data.getDistCellsMapAlphaKey();
         Map<Integer, Integer> plateVtoAMap = data.getPlateVtoAMap();
         Map<Integer, Integer> plateVtoBMap = data.getPlateVtoBMap();
-        Map<Integer, Integer> allAlphas = data.getAllAlphas();
-        Map<Integer, Integer> allBetas = data.getAllBetas();
         Map<Integer, Integer> alphaWellCounts = data.getAlphaWellCounts();
         Map<Integer, Integer> betaWellCounts = data.getBetaWellCounts();
-        Integer alphaCount = allAlphas.size();
-        Integer betaCount = allBetas.size();
         SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph = data.getGraph();
 
 

src/main/java/UserInterface.java

@@ -533,6 +533,8 @@ public class UserInterface {
         }
         //read object data from file
         GraphDataObjectReader dataReader = new GraphDataObjectReader(dataFile);
+        System.out.println("Reading data from file. This may take some time");
+        System.out.println("Time to read file is not included in simulation time data");
         GraphWithMapData data = dataReader.getData();
         //set source file name
         data.setSourceFilename(dataFile);