Add plate well concentrations to output data

src/main/java/Plate.java

@@ -21,7 +21,6 @@ public class Plate {
         this.size = size;
         this.error = error;
         this.concentrations = concentrations;
-        //this.stdDev = stdDev;
         wells = new ArrayList<>();
     }
 

src/main/java/Simulator.java

@@ -159,7 +159,7 @@ public class Simulator {
         SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph = data.getGraph();
 
         //Filter by overlap size
-        if(verbose){System.out.println("Eliminating edges with weights less than" + minOverlapPercent.toString() +
+        if(verbose){System.out.println("Eliminating edges with weights less than " + minOverlapPercent.toString() +
                 " percent of vertex occupancy value.");}
         filterByOverlapSize(graph, alphaWellCounts, betaWellCounts, plateVtoAMap, plateVtoBMap, minOverlapPercent);
         if(verbose){System.out.println("Edges with weights too far below vertex occupancy values set to 0.0");}
@@ -240,13 +240,18 @@ public class Simulator {
         BigDecimal attemptRateTrunc = new BigDecimal(attemptRate, mc);
         double pairingErrorRate = (double) falseCount / (trueCount + falseCount);
         BigDecimal pairingErrorRateTrunc = new BigDecimal(pairingErrorRate, mc);
-        Integer[] wellConcentrations = data.getWellConcentrations();
-        String concentrations = wellConcentrations[0].toString();
-        for (int i = 1; i < wellConcentrations.length; i++) {
-            concentrations = concentrations.concat(", "+ wellConcentrations[i].toString());
+        //make list of well concentrations
+        List<Integer> wellConcentrations = Arrays.asList(data.getWellConcentrations());
+        //make string out of concentrations list
+        StringBuilder concen = new StringBuilder();
+        for(Integer i: wellConcentrations){
+            concen.append(i.toString());
+            concen.append(" ");
         }
+        String concenString = concen.toString();
+
         List<String> comments = new ArrayList<>();
-        comments.add("T cell counts in sample plate wells: " + concentrations);
+        comments.add("T cell counts in sample plate wells: " + concenString);
         comments.add("Total alphas found: " + alphaCount);
         comments.add("Total betas found: " + betaCount);
         comments.add("High overlap threshold: " + highThreshold);

src/main/java/UserInterface.java

@@ -375,7 +375,7 @@ public class UserInterface {
             System.out.println("    * selected from a statistical distribution of distinct cells");
             System.out.println("    * with a set dropout rate for individual sequences within a cell");
             System.out.println("\nMaking a sample plate requires a population of distinct cells");
-            System.out.println("Please enter name of an existing cell sample file: ");
+            System.out.print("Please enter name of an existing cell sample file: ");
             cellFile = sc.next();
             System.out.println("\nThe sample plate will be written to a CSV file");
             System.out.print("Please enter a name for the output file: ");
@@ -530,11 +530,11 @@ public class UserInterface {
             System.out.print("Please enter a name for the output file: ");
             filename = sc.next();
             System.out.println("Bipartite graph can be pre-filtered for relative alpha/beta occupancy.");
-            System.out.println("(To skip pre-filtering: enter number of wells on the sample plate used to make graph)");
+            System.out.println("(To skip pre-filtering: enter number of wells on the plate used to make graph)");
             System.out.println("What is the maximum difference in alpha/beta occupancy to attempt matching?");
             maxOccupancyDiff = sc.nextInt();
             System.out.println("Bipartite graph can be pre-filtered for pair well overlap percentage");
-            System.out.println("(To skip pre-filtering: enter 0");
+            System.out.println("(To skip pre-filtering: enter 0)");
             System.out.println("What is the minimum overlap percentage to attempt matching? (0 - 100)");
             minOverlapPercent = sc.nextInt();
             if (minOverlapPercent < 0 || minOverlapPercent > 100) {