- if (MessageManager.getString("action.search").equals(name))
- {
- searchAlignment = arg.getValue().equals(
- MessageManager.getString(JackHMMER.THIS_ALIGNMENT_KEY));
- }
- else if (MessageManager.getString(DATABASE_KEY).equals(name))
- {
- dbPath = arg.getValue();
- int pos = dbPath.lastIndexOf(File.separator);
- databaseName = dbPath.substring(pos + 1);
- databaseFile = new File(dbPath);
- }
- else if (MessageManager.getString(REPORTING_CUTOFF_KEY)