/**
   * 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);
  }
    private void add(PptTopLevel ppt, ValueTuple vt) {
      // Add the sample to any splitters
      if (ppt.has_splitters()) {
        for (PptSplitter ppt_split : ppt.splitters) {
          PptConditional ppt_cond = ppt_split.choose_conditional(vt);
          if (ppt_cond != null) add(ppt_cond, vt);
          else debug.fine(": sample doesn't pick conditional");
        }
      }

      // if this is a numbered exit, apply to the combined exit as well
      if (!(ppt instanceof PptConditional) && ppt.ppt_name.isNumberedExitPoint()) {
        PptTopLevel parent = all_ppts.get(ppt.ppt_name.makeExit());
        if (parent != null) {
          parent.get_missingOutOfBounds(ppt, vt);
          add(parent, vt);
        }
      }

      // If the point has no variables, skip it
      if (ppt.var_infos.length == 0) return;

      // We should have received sample here before, or there is nothing
      // to check.
      // Yoav added: It can be that the different dtrace and inv files have different program points
      if (false && ppt.num_samples() <= 0)
        Assert.assertTrue(
            ppt.num_samples() > 0,
            "ppt " + ppt.name + " has 0 samples and " + ppt.var_infos.length + " variables");

      // Loop through each slice
      slice_loop:
      for (Iterator<PptSlice> i = ppt.views_iterator(); i.hasNext(); ) {
        PptSlice slice = i.next();
        if (debug_detail.isLoggable(Level.FINE))
          debug_detail.fine(
              ": processing slice " + slice + "vars: " + Debug.toString(slice.var_infos, vt));

        // If any variables are missing, skip this slice
        for (int j = 0; j < slice.var_infos.length; j++) {
          VarInfo v = slice.var_infos[j];
          int mod = vt.getModified(v);
          if (v.isMissing(vt)) {
            if (debug_detail.isLoggable(Level.FINE))
              debug_detail.fine(": : Skipping slice, " + v.name() + " missing");
            continue slice_loop;
          }
          if (v.missingOutOfBounds()) {
            if (debug_detail.isLoggable(Level.FINE))
              debug.fine(": : Skipping slice, " + v.name() + " out of bounds");
            continue slice_loop;
          }
        }

        // Loop through each invariant
        for (Invariant inv : slice.invs) {
          if (debug_detail.isLoggable(Level.FINE))
            debug_detail.fine(": : Processing invariant: " + inv);
          if (!inv.isActive()) {
            if (debug_detail.isLoggable(Level.FINE))
              debug_detail.fine(": : skipped non-active " + inv);
            continue;
          }

          // Yoav added
          if (!activeInvariants.contains(inv)) {
            // System.out.printf ("skipping invariant %s:%s\n", inv.ppt.name(),
            //                   inv.format());
            continue;
          }

          // String invRep = invariant2str(ppt, inv);
          testedInvariants.add(inv);

          InvariantStatus status = inv.add_sample(vt, 1);
          sample_cnt++;
          if (status != InvariantStatus.NO_CHANGE) {
            LineNumberReader lnr = FileIO.data_trace_state.reader;
            String line = (lnr == null) ? "?" : String.valueOf(lnr.getLineNumber());
            if (!quiet) {
              output_stream.println(
                  "At ppt "
                      + ppt.name
                      + ", Invariant '"
                      + inv.format()
                      + "' invalidated by sample "
                      + Debug.toString(slice.var_infos, vt)
                      + "at line "
                      + line
                      + " in file "
                      + FileIO.data_trace_state.filename);
            }
            failedInvariants.add(inv);
            activeInvariants.remove(inv);
            error_cnt++;
          }
        }
      }
    }