/**
   * Identifies.
   *
   * @param reader the catalog reader.
   * @exception IOException if the catalog cannot be accessed.
   * @exception QueryFailException if the query to the server is failed.
   */
  public void identify(CatalogReader reader) throws IOException, QueryFailException {
    // Starts the polling thread.
    PollingThread thread = new PollingThread();
    thread.start();

    try {
      Variability[] records = getSelectedRecords();

      for (int i = 0; i < records.length; i++) {
        CatalogStar star = records[i].getStar();

        StarList l = reader.read(star.getCoor(), 0.1);
        for (int j = 0; j < l.size(); j++) {
          CatalogStar s = (CatalogStar) l.elementAt(j);

          double radius =
              star.getMaximumPositionErrorInArcsec() + s.getMaximumPositionErrorInArcsec();
          double distance = star.getCoor().getAngularDistanceTo(s.getCoor());

          if (distance < radius / 3600.0)
            // Overwrites the already identified star.
            records[i].setIdentifiedStar(s);
        }
      }
    } finally {
      // Ends the polling thread.
      thread.end();
    }
  }
    /** Runs this thread. */
    public void run() {
      CommonFileChooser file_chooser = new CommonFileChooser();
      file_chooser.setDialogTitle("Choose a directory.");
      file_chooser.setMultiSelectionEnabled(false);
      file_chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);

      if (file_chooser.showSaveDialog(pane) == JFileChooser.APPROVE_OPTION) {
        try {
          File directory = file_chooser.getSelectedFile();
          directory.mkdirs();

          // Outputs the variability XML file.

          String path = FileManager.unitePath(directory.getAbsolutePath(), "package.xml");
          File file = new File(path);
          if (file.exists()) {
            String message = "Overwrite to " + file.getPath() + " ?";
            if (0
                != JOptionPane.showConfirmDialog(
                    pane, message, "Confirmation", JOptionPane.YES_NO_OPTION)) {
              return;
            }
          }

          XmlVariabilityHolder holder = new XmlVariabilityHolder();

          Variability[] records = getSelectedRecords();
          for (int i = 0; i < records.length; i++) {
            XmlVariability variability = new XmlVariability(records[i]);
            holder.addVariability(variability);
          }

          holder.write(file);

          // Copies the report XML document files.

          Hashtable hash_xml = new Hashtable();

          for (int i = 0; i < records.length; i++) {
            XmlMagRecord[] mag_records = records[i].getMagnitudeRecords();
            for (int j = 0; j < mag_records.length; j++)
              hash_xml.put(mag_records[j].getImageXmlPath(), this);
          }

          Vector failed_list = new Vector();

          Enumeration keys = hash_xml.keys();
          while (keys.hasMoreElements()) {
            String xml_path = (String) keys.nextElement();
            try {
              File src_file = desktop.getFileManager().newFile(xml_path);
              File dst_file =
                  new File(FileManager.unitePath(directory.getAbsolutePath(), xml_path));
              if (dst_file.exists() == false) FileManager.copy(src_file, dst_file);
            } catch (Exception exception) {
              failed_list.addElement(xml_path);
            }
          }

          if (failed_list.size() > 0) {
            String header = "Failed to copy the following XML files:";
            MessagesDialog dialog = new MessagesDialog(header, failed_list);
            dialog.show(pane, "Error", JOptionPane.ERROR_MESSAGE);
          }

          // Copies the image files.

          failed_list = new Vector();

          keys = hash_xml.keys();
          while (keys.hasMoreElements()) {
            path = (String) keys.nextElement();
            try {
              XmlInformation info =
                  XmlReport.readInformation(desktop.getFileManager().newFile(path));
              path = info.getImage().getContent();

              File src_file = desktop.getFileManager().newFile(path);
              File dst_file = new File(FileManager.unitePath(directory.getAbsolutePath(), path));
              if (dst_file.exists() == false) FileManager.copy(src_file, dst_file);
            } catch (Exception exception) {
              failed_list.addElement(path);
            }
          }

          if (failed_list.size() > 0) {
            String header = "Failed to copy the following image files:";
            MessagesDialog dialog = new MessagesDialog(header, failed_list);
            dialog.show(pane, "Error", JOptionPane.ERROR_MESSAGE);
          }

          // Creates the sub catalog database.

          try {
            DiskFileSystem file_system =
                new DiskFileSystem(
                    new File(
                        directory.getAbsolutePath(),
                        net.aerith.misao.pixy.Properties.getDatabaseDirectoryName()));
            CatalogDBManager new_manager = new GlobalDBManager(file_system).getCatalogDBManager();

            Hashtable hash_stars = new Hashtable();
            for (int i = 0; i < records.length; i++) {
              CatalogStar star = records[i].getStar();

              CatalogDBReader reader =
                  new CatalogDBReader(desktop.getDBManager().getCatalogDBManager());
              StarList list = reader.read(star.getCoor(), 0.5);
              for (int j = 0; j < list.size(); j++) {
                CatalogStar s = (CatalogStar) list.elementAt(j);
                hash_stars.put(s.getOutputString(), s);
              }
            }

            keys = hash_stars.keys();
            while (keys.hasMoreElements()) {
              String string = (String) keys.nextElement();
              CatalogStar star = (CatalogStar) hash_stars.get(string);
              new_manager.addElement(star);
            }
          } catch (Exception exception) {
            String message = "Failed to create sub catalog database.";
            JOptionPane.showMessageDialog(pane, message, "Error", JOptionPane.ERROR_MESSAGE);
          }

          String message = "Completed.";
          JOptionPane.showMessageDialog(pane, message);
        } catch (IOException exception) {
          String message = "Failed.";
          JOptionPane.showMessageDialog(pane, message, "Error", JOptionPane.ERROR_MESSAGE);
        }
      }
    }