Clean up interactive text, bugfix

src/main/java/Simulator.java

@@ -72,9 +72,9 @@ public class Simulator {
         Map<Integer, Integer> allAlphas = samplePlate.assayWellsPeptideP(alphaIndex);
         Map<Integer, Integer> allBetas = samplePlate.assayWellsPeptideP(betaIndex);
         int alphaCount = allAlphas.size();
-        if(verbose){System.out.println("all alphas count: " + alphaCount);}
+        if(verbose){System.out.println("All alphas count: " + alphaCount);}
         int betaCount = allBetas.size();
-        if(verbose){System.out.println("all betas count: " + betaCount);}
+        if(verbose){System.out.println("All betas count: " + betaCount);}
 
         if(verbose){System.out.println("Well maps made");}
 
@@ -87,9 +87,9 @@ public class Simulator {
         filterByOccupancyThreshold(allBetas, lowThreshold, numWells - 1);
         if(verbose){System.out.println("Peptides removed");}
         int pairableAlphaCount = allAlphas.size();
-        if(verbose){System.out.println("Remaining alpha count: " + pairableAlphaCount);}
+        if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
         int pairableBetaCount = allBetas.size();
-        if(verbose){System.out.println("Remaining beta count: " + pairableBetaCount);}
+        if(verbose){System.out.println("Remaining betas count: " + pairableBetaCount);}
 
         if(verbose){System.out.println("Making vertex maps");}
         //For the SimpleWeightedBipartiteGraphMatrixGenerator, all vertices must have
@@ -119,10 +119,10 @@ public class Simulator {
         double[][] weights = new double[plateVtoAMap.size()][plateVtoBMap.size()];
         countPeptidesAndFillMatrix(samplePlate, allAlphas, allBetas, plateAtoVMap,
                 plateBtoVMap, alphaIndex, betaIndex, alphaWellCounts, betaWellCounts, weights);
-        if(verbose){System.out.println("matrix created");}
+        if(verbose){System.out.println("Matrix created");}
 
         //create bipartite graph
-        if(verbose){System.out.println("creating graph");}
+        if(verbose){System.out.println("Creating graph");}
         //the graph object
         SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph =
                 new SimpleWeightedGraph<>(DefaultWeightedEdge.class);

src/main/java/UserInterface.java

@@ -351,7 +351,7 @@ public class UserInterface {
 //        writer.writePlateFile();
 //    }
 
-    //method to output a CSV of sample plate
+    //Output a CSV of sample plate
     private static void makePlate() {
         String cellFile = null;
         String filename = null;
@@ -454,6 +454,7 @@ public class UserInterface {
         }
     }
 
+    //Output serialized binary of GraphAndMapData object
     private static void makeCDR3Graph() {
         String filename = null;
         String cellFile = null;
@@ -462,7 +463,7 @@ public class UserInterface {
         Integer highThreshold = Integer.MAX_VALUE;
         try {
             String str = "\nGenerating bipartite weighted graph encoding occupancy data requires ";
-            str.concat("a cell sample file and a sample plate file.");
+            str = str.concat("a cell sample file and a sample plate file.");
             System.out.println(str);
             System.out.print("Please enter name of an existing cell sample file: ");
             cellFile = sc.next();
@@ -500,10 +501,13 @@ public class UserInterface {
             List<Integer[]> cells = cellReader.getCells();
             GraphWithMapData data = Simulator.makeGraph(cells, plate, lowThreshold, highThreshold, true);
             GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
+            System.out.println("Writing graph and occupancy data to file. This may take some time.");
+            System.out.println("Time to write file is not included in simulation time data.");
             dataWriter.writeDataToFile();
         }
     }
 
+    //Simulate matching and output CSV file of results
     private static void matchCDR3s() throws IOException {
         String filename = null;
         String dataFile = null;
@@ -516,6 +520,13 @@ public class UserInterface {
             System.out.println("The matching results will be written to a file.");
             System.out.print("Please enter a name for the output file: ");
             filename = sc.next();
+            System.out.println("What is the maximum difference in alpha/beta occupancy to attempt matching?");
+            maxOccupancyDiff = sc.nextInt();
+            System.out.println("What is the minimum overlap percentage to attempt matching? (0 - 100)");
+            minOverlapPercent = sc.nextInt();
+            if (minOverlapPercent < 0 || minOverlapPercent > 100) {
+                throw new InputMismatchException("Value outside range. Minimum percent set to 0");
+            }
         } catch (InputMismatchException ex) {
             System.out.println(ex);
             sc.next();
@@ -529,6 +540,7 @@ public class UserInterface {
         MatchingResult results = Simulator.matchCDR3s(data, maxOccupancyDiff, minOverlapPercent, true);
         //write results to file
         MatchingFileWriter writer = new MatchingFileWriter(filename, results);
+        System.out.println("Writing results to file");
         writer.writeResultsToFile();
     }