private SWCDocument readDocument(CommandLineArguments cmd) throws FileNotFoundException { Scanner scanner = cmd.getInputFile() != null ? new Scanner(new File(cmd.getInputFile())) : new Scanner(System.in); StringBuilder sb = new StringBuilder(); while (scanner.hasNextLine()) { sb.append(scanner.nextLine() + "\n"); } scanner.close(); SWCDocument doc = new SWCDocument(sb.toString()); doc.parse(cmd.getParseOptions()); return doc; }