Correct propogation of peptide counts

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);