Add optional stdout print flags

src/main/java/CommandLineInterface.java

@@ -194,6 +194,27 @@ public class CommandLineInterface {
                         System.out.println(k + ": " + result.getMetadata().get(k));
                     }
                 }
+                if(line.hasOption("print-error")) {
+                    System.out.println("pairing error rate: " + result.getPairingErrorRate());
+                }
+                if(line.hasOption("print-attempt")) {
+                    System.out.println("pairing attempt rate: " +result.getPairingAttemptRate());
+                }
+                if(line.hasOption("print-correct")) {
+                    System.out.println("correct pairings: " + result.getCorrectPairingCount());
+                }
+                if(line.hasOption("print-incorrect")) {
+                    System.out.println("incorrect pairings: " + result.getIncorrectPairingCount());
+                }
+                if(line.hasOption("print-alphas")) {
+                    System.out.println("total alphas found: " + result.getAlphaCount());
+                }
+                if(line.hasOption("print-betas")) {
+                    System.out.println("total betas found: " + result.getBetaCount());
+                }
+                if(line.hasOption("print-time")) {
+                    System.out.println("simulation time (seconds): " + result.getSimulationTime());
+                }
             }
         }
         catch (ParseException exp) {
@@ -413,22 +434,32 @@ public class CommandLineInterface {
                 .addOption(outputFile);
 
         //options for output to System.out
-//       Option printErrorRate = Option.builder().longOpt("print-error")
-//               .desc("(Optional) Print the pairing error rate to stdout").build();
-//       Option printAttempt = Option.builder().longOpt("print-attempt")
-//               .desc("(Optional) Print the pairing attempt rate to stdout").build();
-//       Option printCorrect = Option.builder().longOpt("print-correct")
-//               .desc("(Optional) Print the number of correct pairs to stdout").build();
-//       Option printIncorrect = Option.builder().longOpt("print-incorrect")
-//               .desc("(Optional) Print the number of incorrect pairs to stdout").build();
-       Option printMetadata = Option.builder().longOpt("print-metadata")
-                       .desc("(Optional) Print summary of matching results to stdout.").build();
+        Option printAlphaCount = Option.builder().longOpt("print-alphas")
+                .desc("(Optional) Print the number of distinct alpha sequences to stdout.").build();
+        Option printBetaCount = Option.builder().longOpt("print-betas")
+                .desc("(Optional) Print the number of distinct beta sequences to stdout.").build();
+        Option printTime = Option.builder().longOpt("print-time")
+                .desc("(Optional) Print the total simulation time to stdout.").build();
+        Option printErrorRate = Option.builder().longOpt("print-error")
+               .desc("(Optional) Print the pairing error rate to stdout").build();
+        Option printAttempt = Option.builder().longOpt("print-attempt")
+               .desc("(Optional) Print the pairing attempt rate to stdout").build();
+        Option printCorrect = Option.builder().longOpt("print-correct")
+               .desc("(Optional) Print the number of correct pairs to stdout").build();
+        Option printIncorrect = Option.builder().longOpt("print-incorrect")
+               .desc("(Optional) Print the number of incorrect pairs to stdout").build();
+        Option printMetadata = Option.builder().longOpt("print-metadata")
+                       .desc("(Optional) Print a full summary of the matching results to stdout.").build();
+
        matchCDR3options
-//               .addOption(printErrorRate)
-//               .addOption(printAttempt)
-//               .addOption(printCorrect)
-//               .addOption(printIncorrect)
-               .addOption(printMetadata);
+               .addOption(printErrorRate)
+               .addOption(printAttempt)
+               .addOption(printCorrect)
+               .addOption(printIncorrect)
+               .addOption(printMetadata)
+               .addOption(printAlphaCount)
+               .addOption(printBetaCount)
+               .addOption(printTime);
         return matchCDR3options;
     }
 

src/main/java/GraphDataObjectReader.java

@@ -21,6 +21,7 @@ public class GraphDataObjectReader {
             }
             data = (GraphWithMapData) in.readObject();
         } catch (FileNotFoundException | ClassNotFoundException ex) {
+            System.out.println("Graph/data file " + filename + " not found.");
             ex.printStackTrace();
         }
     }