/**
  * This does the work of main, but it never calls System.exit, so it is appropriate to be called
  * progrmmatically. Termination of the program with a message to the user is indicated by throwing
  * Daikon.TerminationMessage.
  *
  * @see #main(String[])
  * @see daikon.Daikon.TerminationMessage
  */
 public static void mainHelper(final String[] args)
     throws FileNotFoundException, IOException, ClassNotFoundException {
   daikon.LogHelper.setupLogs(daikon.LogHelper.INFO);
   LongOpt[] longopts =
       new LongOpt[] {
         new LongOpt(Daikon.suppress_redundant_SWITCH, LongOpt.NO_ARGUMENT, null, 0),
         new LongOpt(Daikon.config_option_SWITCH, LongOpt.REQUIRED_ARGUMENT, null, 0),
         new LongOpt(Daikon.debugAll_SWITCH, LongOpt.NO_ARGUMENT, null, 0),
         new LongOpt(Daikon.debug_SWITCH, LongOpt.REQUIRED_ARGUMENT, null, 0),
       };
   Getopt g = new Getopt("daikon.ExtractConsequent", args, "h", longopts);
   int c;
   while ((c = g.getopt()) != -1) {
     switch (c) {
       case 0:
         // got a long option
         String option_name = longopts[g.getLongind()].getName();
         if (Daikon.help_SWITCH.equals(option_name)) {
           System.out.println(usage);
           throw new Daikon.TerminationMessage();
         } else if (Daikon.suppress_redundant_SWITCH.equals(option_name)) {
           Daikon.suppress_redundant_invariants_with_simplify = true;
         } else if (Daikon.config_option_SWITCH.equals(option_name)) {
           String item = Daikon.getOptarg(g);
           daikon.config.Configuration.getInstance().apply(item);
           break;
         } else if (Daikon.debugAll_SWITCH.equals(option_name)) {
           Global.debugAll = true;
         } else if (Daikon.debug_SWITCH.equals(option_name)) {
           LogHelper.setLevel(Daikon.getOptarg(g), LogHelper.FINE);
         } else {
           throw new RuntimeException("Unknown long option received: " + option_name);
         }
         break;
       case 'h':
         System.out.println(usage);
         throw new Daikon.TerminationMessage();
       case '?':
         break; // getopt() already printed an error
       default:
         System.out.println("getopt() returned " + c);
         break;
     }
   }
   // The index of the first non-option argument -- the name of the file
   int fileIndex = g.getOptind();
   if (args.length - fileIndex != 1) {
     throw new Daikon.TerminationMessage("Wrong number of arguments." + Daikon.lineSep + usage);
   }
   String filename = args[fileIndex];
   PptMap ppts =
       FileIO.read_serialized_pptmap(
           new File(filename), true // use saved config
           );
   extract_consequent(ppts);
 }
 /**
  * This function allows this test to be run from the command line instead of its usual method,
  * which is through the Daikon MasterTester.
  *
  * @param args arguments to the main function, which control options to the program. As of now
  *     there is only one option, "--generate_goals", which will generate goal information for the
  *     selected tests assuming the output that the tests provide is the correct output
  */
 public static void main(String[] args) {
   daikon.LogHelper.setupLogs(daikon.LogHelper.INFO);
   if (args.length == 1 && args[0].equalsIgnoreCase("--generate_goals")) {
     writeCommandFile();
   } else if (args.length > 0) {
     throw new Daikon.TerminationMessage(
         "Usage: java daikon.test.InvariantAddAndCheckTester" + " [--generate_goals]");
   } else {
     junit.textui.TestRunner.run(new TestSuite(InvariantAddAndCheckTester.class));
   }
 }
  /**
   * This does the work of main, but it never calls System.exit, so it is appropriate to be called
   * progrmmatically. Termination of the program with a message to the user is indicated by throwing
   * Daikon.TerminationMessage.
   *
   * @see #main(String[])
   * @see daikon.Daikon.TerminationMessage
   */
  public static void mainHelper(final String[] args)
      throws FileNotFoundException, StreamCorruptedException, OptionalDataException, IOException,
          ClassNotFoundException {
    daikon.LogHelper.setupLogs(daikon.LogHelper.INFO);

    LongOpt[] longopts =
        new LongOpt[] {
          new LongOpt(Daikon.config_option_SWITCH, LongOpt.REQUIRED_ARGUMENT, null, 0),
          new LongOpt(output_SWITCH, LongOpt.REQUIRED_ARGUMENT, null, 0),
          new LongOpt(dir_SWITCH, LongOpt.REQUIRED_ARGUMENT, null, 0),
          new LongOpt(conf_SWITCH, LongOpt.NO_ARGUMENT, null, 0),
          new LongOpt(filter_SWITCH, LongOpt.NO_ARGUMENT, null, 0),
          new LongOpt(Daikon.debugAll_SWITCH, LongOpt.NO_ARGUMENT, null, 0),
          new LongOpt(Daikon.debug_SWITCH, LongOpt.REQUIRED_ARGUMENT, null, 0),
          new LongOpt(Daikon.ppt_regexp_SWITCH, LongOpt.REQUIRED_ARGUMENT, null, 0),
          new LongOpt(Daikon.track_SWITCH, LongOpt.REQUIRED_ARGUMENT, null, 0),
        };
    Getopt g = new Getopt("daikon.tools.InvariantChecker", args, "h", longopts);
    int c;
    while ((c = g.getopt()) != -1) {
      switch (c) {
        case 0:
          // got a long option
          String option_name = longopts[g.getLongind()].getName();
          if (Daikon.help_SWITCH.equals(option_name)) {
            System.out.println(usage);
            throw new Daikon.TerminationMessage();
          } else if (conf_SWITCH.equals(option_name)) {
            doConf = true;
          } else if (filter_SWITCH.equals(option_name)) {
            doFilter = true;
          } else if (dir_SWITCH.equals(option_name)) {
            dir_file = new File(g.getOptarg());
            if (!dir_file.exists() || !dir_file.isDirectory())
              throw new Daikon.TerminationMessage("Error reading the directory " + dir_file);

          } else if (output_SWITCH.equals(option_name)) {
            output_file = new File(g.getOptarg());
            output_stream = new PrintStream(new FileOutputStream(output_file));
          } else if (Daikon.config_option_SWITCH.equals(option_name)) {
            String item = g.getOptarg();
            daikon.config.Configuration.getInstance().apply(item);
            break;
          } else if (Daikon.debugAll_SWITCH.equals(option_name)) {
            Global.debugAll = true;
          } else if (Daikon.debug_SWITCH.equals(option_name)) {
            LogHelper.setLevel(g.getOptarg(), LogHelper.FINE);
          } else if (Daikon.track_SWITCH.equals(option_name)) {
            LogHelper.setLevel("daikon.Debug", LogHelper.FINE);
            String error = Debug.add_track(g.getOptarg());
            if (error != null) {
              throw new Daikon.TerminationMessage(
                  "Error parsing track argument '" + g.getOptarg() + "' - " + error);
            }
          } else {
            throw new RuntimeException("Unknown long option received: " + option_name);
          }
          break;
        case 'h':
          System.out.println(usage);
          throw new Daikon.TerminationMessage();
        case '?':
          break; // getopt() already printed an error
        default:
          System.out.println("getopt() returned " + c);
          break;
      }
    }

    // Loop through each filename specified
    for (int i = g.getOptind(); i < args.length; i++) {

      // Get the file and make sure it exists
      File file = new File(args[i]);
      if (!file.exists()) {
        throw new Error("File " + file + " not found.");
      }

      // These aren't "endsWith()" because there might be a suffix on the end
      // (eg, a date).
      String filename = file.toString();
      if (filename.indexOf(".inv") != -1) {
        if (inv_file != null) {
          throw new Daikon.TerminationMessage("multiple inv files specified", usage);
        }
        inv_file = file;
      } else if (filename.indexOf(".dtrace") != -1) {
        dtrace_files.add(filename);
      } else {
        throw new Error("Unrecognized argument: " + file);
      }
    }
    if (dir_file == null) {
      checkInvariants();
      return;
    }

    // Yoav additions:
    File[] filesInDir = dir_file.listFiles();
    if (filesInDir == null || filesInDir.length == 0)
      throw new Daikon.TerminationMessage("The directory " + dir_file + " is empty", usage);
    ArrayList<File> invariants = new ArrayList<File>();
    for (File f : filesInDir) if (f.toString().indexOf(".inv") != -1) invariants.add(f);
    if (invariants.size() == 0)
      throw new Daikon.TerminationMessage(
          "Did not find any invariant files in the directory " + dir_file, usage);
    ArrayList<File> dtraces = new ArrayList<File>();
    for (File f : filesInDir) if (f.toString().indexOf(".dtrace") != -1) dtraces.add(f);
    if (dtraces.size() == 0)
      throw new Daikon.TerminationMessage(
          "Did not find any dtrace files in the directory " + dir_file, usage);

    System.out.println(
        "Collecting data for invariants files " + invariants + " and dtrace files " + dtraces);

    dtrace_files.clear();
    for (File dtrace : dtraces) {
      dtrace_files.add(dtrace.toString());
    }

    String commaLine = "";
    for (File inFile : invariants) {
      String name = inFile.getName().replace(".inv", "").replace(".gz", "");
      commaLine += "," + name;
    }
    outputComma.add(commaLine);

    commaLine = "";
    for (File inFile : invariants) {
      inv_file = inFile;
      failedInvariants.clear();
      testedInvariants.clear();
      error_cnt = 0;

      output_stream =
          new PrintStream(
              new FileOutputStream(
                  inFile.toString().replace(".inv", "").replace(".gz", "")
                      + ".false-positives.txt"));
      checkInvariants();
      output_stream.close();

      int failedCount = failedInvariants.size();
      int testedCount = testedInvariants.size();
      String percent = toPercentage(failedCount, testedCount);
      commaLine += "," + percent;
    }
    outputComma.add(commaLine);

    System.out.println();
    for (String output : outputComma) System.out.println(output);
  }