Example usage for java.io InputStreamReader InputStreamReader

List of usage examples for java.io InputStreamReader InputStreamReader

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Introduction

In this page you can find the example usage for java.io InputStreamReader InputStreamReader.

Prototype

public InputStreamReader(InputStream in)

Source Link

Document

Creates an InputStreamReader that uses the default charset.

Usage

From source file:cc.twittertools.util.ExtractSubcollection.java

@SuppressWarnings("static-access")
public static void main(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(OptionBuilder.withArgName("dir").hasArg().withDescription("source collection directory")
            .create(COLLECTION_OPTION));
    options.addOption(//from  ww  w.  j a v a 2s. com
            OptionBuilder.withArgName("file").hasArg().withDescription("list of tweetids").create(ID_OPTION));

    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();
    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }

    if (!cmdline.hasOption(COLLECTION_OPTION) || !cmdline.hasOption(ID_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(ExtractSubcollection.class.getName(), options);
        System.exit(-1);
    }

    String collectionPath = cmdline.getOptionValue(COLLECTION_OPTION);

    LongOpenHashSet tweetids = new LongOpenHashSet();
    File tweetidsFile = new File(cmdline.getOptionValue(ID_OPTION));
    if (!tweetidsFile.exists()) {
        System.err.println("Error: " + tweetidsFile + " does not exist!");
        System.exit(-1);
    }
    LOG.info("Reading tweetids from " + tweetidsFile);

    FileInputStream fin = new FileInputStream(tweetidsFile);
    BufferedReader br = new BufferedReader(new InputStreamReader(fin));

    String s;
    while ((s = br.readLine()) != null) {
        tweetids.add(Long.parseLong(s));
    }
    br.close();
    fin.close();
    LOG.info("Read " + tweetids.size() + " tweetids.");

    File file = new File(collectionPath);
    if (!file.exists()) {
        System.err.println("Error: " + file + " does not exist!");
        System.exit(-1);
    }

    PrintStream out = new PrintStream(System.out, true, "UTF-8");
    StatusStream stream = new JsonStatusCorpusReader(file);
    Status status;
    while ((status = stream.next()) != null) {
        if (tweetids.contains(status.getId())) {
            out.println(status.getJsonObject().toString());
        }
    }
    stream.close();
    out.close();
}

From source file:org.mzd.shap.spring.cli.ConfigSetup.java

public static void main(String[] args) {
    // check args
    if (args.length != 1) {
        exitOnError(1, null);/*from   w  w  w.j  ava  2s  .  c o  m*/
    }

    // check file existance
    File analyzerXML = new File(args[0]);
    if (!analyzerXML.exists()) {
        exitOnError(1, "'" + analyzerXML.getPath() + "' did not exist\n");
    }

    // prompt user whether existing data should be purged
    boolean isPurged = false;
    String ormContext = null;
    BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
    try {
        System.out.println("\nDo you wish to purge the database before running setup?");
        System.out.println("WARNING: all existing data in SHAP will be lost!");
        System.out.println("Really purge? yes/[NO]");
        String ans = br.readLine();
        if (ans.toLowerCase().equals("yes")) {
            System.out.println("Purging enabled");
            ormContext = "orm-purge-context.xml";
            isPurged = true;
        } else {
            System.out.println("Purging disabled");
            ormContext = "orm-context.xml";
        }
    } catch (IOException ex) {
        throw new RuntimeException(ex);
    }

    // run tool
    try {
        // Using a generic application context since we're referencing
        // both classpath and filesystem resources.
        GenericApplicationContext ctx = new GenericApplicationContext();
        XmlBeanDefinitionReader xmlReader = new XmlBeanDefinitionReader(ctx);
        xmlReader.loadBeanDefinitions(new ClassPathResource("datasource-context.xml"),
                new ClassPathResource(ormContext), new FileSystemResource(analyzerXML));
        ctx.refresh();

        /*
         * Create an base admin user.
         */
        if (isPurged) {
            //only attempted if we've wiped the old database.
            RoleDao roleDao = (RoleDao) ctx.getBean("roleDao");
            Role adminRole = roleDao.saveOrUpdate(new Role("admin", "ROLE_ADMIN"));
            Role userRole = roleDao.saveOrUpdate(new Role("user", "ROLE_USER"));
            UserDao userDao = (UserDao) ctx.getBean("userDao");
            userDao.saveOrUpdate(new User("admin", "admin", "shap01", adminRole, userRole));
        }

        /*
         * Create some predefined analyzers. Users should have modified
         * the configuration file to suit their environment.
         */
        AnnotatorDao annotatorDao = (AnnotatorDao) ctx.getBean("annotatorDao");
        DetectorDao detectorDao = (DetectorDao) ctx.getBean("detectorDao");

        ConfigSetup config = (ConfigSetup) ctx.getBean("configuration");

        for (Annotator an : config.getAnnotators()) {
            System.out.println("Adding annotator: " + an.getName());
            annotatorDao.saveOrUpdate(an);
        }

        for (Detector dt : config.getDetectors()) {
            System.out.println("Adding detector: " + dt.getName());
            detectorDao.saveOrUpdate(dt);
        }

        System.exit(0);
    } catch (Throwable t) {
        System.err.println(t.getMessage());
        System.exit(1);
    }
}

From source file:com.genentech.struchk.OEMDLPercieveChecker.java

public static void main(String[] args) throws ParseException, JDOMException, IOException {
    // create command line Options object
    Options options = new Options();
    Option opt = new Option("i", true, "input file [.ism,.sdf,...]");
    opt.setRequired(true);/*from w  ww  .  ja v a  2 s  .c o m*/
    options.addOption(opt);

    opt = new Option("o", true, "output file");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("d", false, "debug: wait for user to press key at startup.");
    opt.setRequired(false);
    options.addOption(opt);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        exitWithHelp(options);
    }
    args = cmd.getArgs();

    if (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    if (args.length != 0) {
        exitWithHelp(options);
    }

    String inFile = cmd.getOptionValue("i");
    String outFile = cmd.getOptionValue("o");

    OEMDLPercieveChecker checker = null;
    try {
        checker = new OEMDLPercieveChecker();

        oemolostream out = new oemolostream(outFile);
        oemolistream in = new oemolistream(inFile);

        OEGraphMol mol = new OEGraphMol();
        while (oechem.OEReadMolecule(in, mol)) {
            if (!checker.checkMol(mol))
                oechem.OEWriteMolecule(out, mol);
        }
        checker.delete();
        in.close();
        in.delete();

        out.close();
        out.delete();

    } catch (Exception e) {
        throw new Error(e);
    }
    System.err.println("Done:");
}

From source file:cc.twittertools.util.VerifySubcollection.java

@SuppressWarnings("static-access")
public static void main(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(OptionBuilder.withArgName("dir").hasArg().withDescription("source collection directory")
            .create(COLLECTION_OPTION));
    options.addOption(//  www .  j  ava2s. com
            OptionBuilder.withArgName("file").hasArg().withDescription("list of tweetids").create(ID_OPTION));

    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();
    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }

    if (!cmdline.hasOption(COLLECTION_OPTION) || !cmdline.hasOption(ID_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(ExtractSubcollection.class.getName(), options);
        System.exit(-1);
    }

    String collectionPath = cmdline.getOptionValue(COLLECTION_OPTION);

    LongOpenHashSet tweetids = new LongOpenHashSet();
    File tweetidsFile = new File(cmdline.getOptionValue(ID_OPTION));
    if (!tweetidsFile.exists()) {
        System.err.println("Error: " + tweetidsFile + " does not exist!");
        System.exit(-1);
    }
    LOG.info("Reading tweetids from " + tweetidsFile);

    FileInputStream fin = new FileInputStream(tweetidsFile);
    BufferedReader br = new BufferedReader(new InputStreamReader(fin));

    String s;
    while ((s = br.readLine()) != null) {
        tweetids.add(Long.parseLong(s));
    }
    br.close();
    fin.close();
    LOG.info("Read " + tweetids.size() + " tweetids.");

    File file = new File(collectionPath);
    if (!file.exists()) {
        System.err.println("Error: " + file + " does not exist!");
        System.exit(-1);
    }

    LongOpenHashSet seen = new LongOpenHashSet();
    TreeMap<Long, String> tweets = Maps.newTreeMap();

    PrintStream out = new PrintStream(System.out, true, "UTF-8");
    StatusStream stream = new JsonStatusCorpusReader(file);
    Status status;
    int cnt = 0;
    while ((status = stream.next()) != null) {
        if (!tweetids.contains(status.getId())) {
            LOG.error("tweetid " + status.getId() + " doesn't belong in collection");
            continue;
        }
        if (seen.contains(status.getId())) {
            LOG.error("tweetid " + status.getId() + " already seen!");
            continue;
        }

        tweets.put(status.getId(), status.getJsonObject().toString());
        seen.add(status.getId());
        cnt++;
    }
    LOG.info("total of " + cnt + " tweets in subcollection.");

    for (Map.Entry<Long, String> entry : tweets.entrySet()) {
        out.println(entry.getValue());
    }

    stream.close();
    out.close();
}

From source file:edu.cmu.lti.oaqa.apps.Client.java

public static void main(String args[]) {
    BufferedReader inp = new BufferedReader(new InputStreamReader(System.in));

    Options opt = new Options();

    Option o = new Option(PORT_SHORT_PARAM, PORT_LONG_PARAM, true, PORT_DESC);
    o.setRequired(true);//from   w ww  .  j a v  a  2s .co  m
    opt.addOption(o);
    o = new Option(HOST_SHORT_PARAM, HOST_LONG_PARAM, true, HOST_DESC);
    o.setRequired(true);
    opt.addOption(o);
    opt.addOption(K_SHORT_PARAM, K_LONG_PARAM, true, K_DESC);
    opt.addOption(R_SHORT_PARAM, R_LONG_PARAM, true, R_DESC);
    opt.addOption(QUERY_TIME_SHORT_PARAM, QUERY_TIME_LONG_PARAM, true, QUERY_TIME_DESC);
    opt.addOption(RET_OBJ_SHORT_PARAM, RET_OBJ_LONG_PARAM, false, RET_OBJ_DESC);
    opt.addOption(RET_EXTERN_ID_SHORT_PARAM, RET_EXTERN_ID_LONG_PARAM, false, RET_EXTERN_ID_DESC);

    CommandLineParser parser = new org.apache.commons.cli.GnuParser();

    try {
        CommandLine cmd = parser.parse(opt, args);

        String host = cmd.getOptionValue(HOST_SHORT_PARAM);

        String tmp = null;

        tmp = cmd.getOptionValue(PORT_SHORT_PARAM);

        int port = -1;

        try {
            port = Integer.parseInt(tmp);
        } catch (NumberFormatException e) {
            Usage("Port should be integer!");
        }

        boolean retObj = cmd.hasOption(RET_OBJ_SHORT_PARAM);
        boolean retExternId = cmd.hasOption(RET_EXTERN_ID_SHORT_PARAM);

        String queryTimeParams = cmd.getOptionValue(QUERY_TIME_SHORT_PARAM);
        if (null == queryTimeParams)
            queryTimeParams = "";

        SearchType searchType = SearchType.kKNNSearch;
        int k = 0;
        double r = 0;

        if (cmd.hasOption(K_SHORT_PARAM)) {
            if (cmd.hasOption(R_SHORT_PARAM)) {
                Usage("Range search is not allowed if the KNN search is specified!");
            }
            tmp = cmd.getOptionValue(K_SHORT_PARAM);
            try {
                k = Integer.parseInt(tmp);
            } catch (NumberFormatException e) {
                Usage("K should be integer!");
            }
            searchType = SearchType.kKNNSearch;
        } else if (cmd.hasOption(R_SHORT_PARAM)) {
            if (cmd.hasOption(K_SHORT_PARAM)) {
                Usage("KNN search is not allowed if the range search is specified!");
            }
            searchType = SearchType.kRangeSearch;
            tmp = cmd.getOptionValue(R_SHORT_PARAM);
            try {
                r = Double.parseDouble(tmp);
            } catch (NumberFormatException e) {
                Usage("The range value should be numeric!");
            }
        } else {
            Usage("One has to specify either range or KNN-search parameter");
        }

        String separator = System.getProperty("line.separator");

        StringBuffer sb = new StringBuffer();
        String s;

        while ((s = inp.readLine()) != null) {
            sb.append(s);
            sb.append(separator);
        }

        String queryObj = sb.toString();

        try {
            TTransport transport = new TSocket(host, port);
            transport.open();

            TProtocol protocol = new TBinaryProtocol(transport);
            QueryService.Client client = new QueryService.Client(protocol);

            if (!queryTimeParams.isEmpty())
                client.setQueryTimeParams(queryTimeParams);

            List<ReplyEntry> res = null;

            long t1 = System.nanoTime();

            if (searchType == SearchType.kKNNSearch) {
                System.out.println(String.format("Running a %d-NN search", k));
                res = client.knnQuery(k, queryObj, retExternId, retObj);
            } else {
                System.out.println(String.format("Running a range search (r=%g)", r));
                res = client.rangeQuery(r, queryObj, retExternId, retObj);
            }

            long t2 = System.nanoTime();

            System.out.println(String.format("Finished in %g ms", (t2 - t1) / 1e6));

            for (ReplyEntry e : res) {
                System.out.println(String.format("id=%d dist=%g %s", e.getId(), e.getDist(),
                        retExternId ? "externId=" + e.getExternId() : ""));
                if (retObj)
                    System.out.println(e.getObj());
            }

            transport.close(); // Close transport/socket !
        } catch (TException te) {
            System.err.println("Apache Thrift exception: " + te);
            te.printStackTrace();
        }

    } catch (ParseException e) {
        Usage("Cannot parse arguments");
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(1);
    }
}

From source file:httpclient.UploadAction.java

public static void main(String[] args) throws FileNotFoundException {
    File targetFile1 = new File("F:\\2.jpg");
    // File targetFile2 = new File("F:\\1.jpg");
    FileInputStream fis1 = new FileInputStream(targetFile1);
    // FileInputStream fis2 = new FileInputStream(targetFile2);
    // String targetURL =
    // "http://static.fangbiandian.com.cn/round_server/upload/uploadFile.do";
    String targetURL = "http://www.fangbiandian.com.cn/round_server/user/updateUserInfo.do";
    HttpPost filePost = new HttpPost(targetURL);
    try {//w w w . j  a  v  a2  s  . com
        // ?????
        HttpClient client = new DefaultHttpClient();
        // FormBodyPart fbp1 = new FormBodyPart("file1", new
        // FileBody(targetFile1));
        // FormBodyPart fbp2 = new FormBodyPart("file2", new
        // FileBody(targetFile2));
        // FormBodyPart fbp3 = new FormBodyPart("file3", new
        // FileBody(targetFile3));
        // List<FormBodyPart> picList = new ArrayList<FormBodyPart>();
        // picList.add(fbp1);
        // picList.add(fbp2);
        // picList.add(fbp3);
        Map<String, Object> paramMap = new HashMap<String, Object>();
        paramMap.put("userId", "65478A5CD8D20C3807EE16CF22AF8A17");
        Map<String, Object> map = new HashMap<String, Object>();
        String jsonStr = JSON.toJSONString(paramMap);
        map.put("cid", 321);
        map.put("request", jsonStr);
        String jsonString = JSON.toJSONString(map);
        MultipartEntity multiEntity = new MultipartEntity();
        Charset charset = Charset.forName("UTF-8");
        multiEntity.addPart("request", new StringBody(jsonString, charset));
        multiEntity.addPart("photo", new InputStreamBody(fis1, "2.jpg"));
        // multiEntity.addPart("licenseUrl", new InputStreamBody(fis2,
        // "1.jpg"));
        filePost.setEntity(multiEntity);
        HttpResponse response = client.execute(filePost);
        int code = response.getStatusLine().getStatusCode();
        System.out.println(code);
        if (HttpStatus.SC_OK == code) {
            System.out.println("?");
            HttpEntity entity = response.getEntity();
            if (entity != null) {
                InputStream instream = entity.getContent();
                try {
                    // do something useful
                    BufferedReader reader = new BufferedReader(new InputStreamReader(instream));
                    String str = null;
                    while ((str = reader.readLine()) != null) {
                        System.out.println(str);
                    }
                } finally {
                    instream.close();
                }
            }
        } else {
            System.out.println("");
        }
    } catch (Exception ex) {
        ex.printStackTrace();
    } finally {
        filePost.releaseConnection();
    }
}

From source file:com.janrain.backplane.common.HmacHashUtils.java

public static void main(String[] args) throws IOException {
    String password;//from w  ww  .  ja v  a  2 s  .  co  m
    if (args.length == 1) {
        password = args[0];
    } else {
        System.out.print("Password: ");
        password = new BufferedReader(new InputStreamReader(System.in)).readLine();
    }
    System.out.println("hmac hash: " + hmacHash(password));
}

From source file:edu.scripps.fl.pubchem.app.CIDDownloader.java

public static void main(String[] args) throws Exception {
    CIDDownloader fetcher = new CIDDownloader();

    CommandLineHandler clh = new CommandLineHandler() {
        public void configureOptions(Options options) {
            options.addOption(OptionBuilder.withLongOpt("input_file").withType("").withValueSeparator('=')
                    .hasArg().create());
            options.addOption(OptionBuilder.withLongOpt("output_file").withType("").withValueSeparator('=')
                    .hasArg().isRequired().create());
        }/*  w  w w.  j a  v  a2 s .c o m*/
    };
    args = clh.handle(args);
    String inputFile = clh.getCommandLine().getOptionValue("input_file");
    String outputFile = clh.getCommandLine().getOptionValue("output_file");

    fetcher.setOutputFile(outputFile);
    Iterator<?> iterator;
    if (null == inputFile) {
        if (args.length == 0) {
            log.info("Running query to find CIDs in PCAssayResult but not in PCCompound");
            SQLQuery query = PubChemDB.getSession().createSQLQuery(
                    "select distinct r.cid from pcassay_result r left join pccompound c on r.cid = c.cid where (r.cid is not null and r.cid > 0 ) and c.cid is null order by r.cid");
            ScrollableResults scroll = query.scroll(ScrollMode.FORWARD_ONLY);
            iterator = new ScrollableResultsIterator<Integer>(Integer.class, scroll);
        } else {
            iterator = Arrays.asList(args).iterator();
        }
    } else if ("-".equals(inputFile)) {
        log.info("Reading CIDs (one per line) from STDIN");
        iterator = new LineIterator(new InputStreamReader(System.in));
    } else {
        log.info("Reading CIDs (one per line) from " + inputFile);
        iterator = new LineIterator(new FileReader(inputFile));
    }
    fetcher.process(iterator);
    System.exit(0);
}

From source file:edu.mit.fss.examples.ISSFederate.java

/**
 * The main method. This configures the Orekit data path, creates the 
 * ISS federate objects and launches the associated graphical user 
 * interface./*from w ww .  j  a va  2s .  c  o m*/
 *
 * @param args the arguments
 * @throws RTIexception the RTI exception
 * @throws URISyntaxException 
 */
public static void main(String[] args) throws RTIexception, URISyntaxException {
    BasicConfigurator.configure();

    boolean headless = false;

    logger.debug("Setting Orekit data path.");
    System.setProperty(DataProvidersManager.OREKIT_DATA_PATH,
            new File(ISSFederate.class.getResource("/orekit-data.zip").toURI()).getAbsolutePath());

    logger.trace("Creating federate instance.");
    final ISSFederate federate = new ISSFederate();

    logger.trace("Setting minimum step duration and time step.");
    long timeStep = 60 * 1000, minimumStepDuration = 100;
    federate.setMinimumStepDuration(minimumStepDuration);
    federate.setTimeStep(timeStep);

    try {
        logger.debug("Loading TLE data from file.");
        BufferedReader br = new BufferedReader(new InputStreamReader(
                federate.getClass().getClassLoader().getResourceAsStream("edu/mit/fss/examples/data.tle")));

        final SpaceSystem satellite;
        final SurfaceSystem station1, station2, station3;

        while (br.ready()) {
            if (br.readLine().matches(".*ISS.*")) {
                logger.debug("Found ISS data.");

                logger.trace("Adding FSS supplier space system.");
                satellite = new SpaceSystem("FSS Supplier", new TLE(br.readLine(), br.readLine()), 5123e3);
                federate.addObject(satellite);

                logger.trace("Adding Keio ground station.");
                station1 = new SurfaceSystem("Keio",
                        new GeodeticPoint(FastMath.toRadians(35.551929), FastMath.toRadians(139.647119), 300),
                        satellite.getState().getDate(), 5123e3, 5);
                federate.addObject(station1);

                logger.trace("Adding SkolTech ground station.");
                station2 = new SurfaceSystem("SkolTech",
                        new GeodeticPoint(FastMath.toRadians(55.698679), FastMath.toRadians(37.571994), 200),
                        satellite.getState().getDate(), 5123e3, 5);
                federate.addObject(station2);

                logger.trace("Adding MIT ground station.");
                station3 = new SurfaceSystem("MIT",
                        new GeodeticPoint(FastMath.toRadians(42.360184), FastMath.toRadians(-71.093742), 100),
                        satellite.getState().getDate(), 5123e3, 5);
                federate.addObject(station3);

                try {
                    logger.trace("Setting inital time.");
                    federate.setInitialTime(
                            satellite.getInitialState().getDate().toDate(TimeScalesFactory.getUTC()).getTime());
                } catch (IllegalArgumentException | OrekitException e) {
                    logger.error(e.getMessage());
                    e.printStackTrace();
                }

                if (!headless) {
                    logger.debug("Launching the graphical user interface.");
                    SwingUtilities.invokeAndWait(new Runnable() {
                        @Override
                        public void run() {
                            MemberFrame frame = new MemberFrame(federate,
                                    new MultiComponentPanel(
                                            Arrays.asList(new SpaceSystemPanel(federate, satellite),
                                                    new SurfaceSystemPanel(federate, station1),
                                                    new SurfaceSystemPanel(federate, station2),
                                                    new SurfaceSystemPanel(federate, station3))));
                            frame.pack();
                            frame.setVisible(true);
                        }
                    });
                }

                break;
            }
        }
        br.close();
    } catch (InvocationTargetException | InterruptedException | OrekitException | IOException e) {
        e.printStackTrace();
        logger.fatal(e);
    }

    logger.trace("Setting federate name, type, and FOM path.");
    federate.getConnection().setFederateName("ISS");
    federate.getConnection().setFederateType("FSS Supplier");
    federate.getConnection().setFederationName("FSS");
    federate.getConnection().setFomPath(
            new File(federate.getClass().getClassLoader().getResource("edu/mit/fss/hla/fss.xml").toURI())
                    .getAbsolutePath());
    federate.getConnection().setOfflineMode(false);
    federate.connect();

    if (headless) {
        federate.setMinimumStepDuration(10);
        federate.initialize();
        federate.run();
    }
}

From source file:edu.msu.cme.rdp.graph.sandbox.BloomFilterInterrogator.java

public static void main(String[] args) throws Exception {
    if (args.length != 1) {
        System.err.println("USAGE: BloomFilterStats <bloom_filter>");
        System.exit(1);/*from ww w.j av  a2s  . c o m*/
    }

    File bloomFile = new File(args[0]);

    ObjectInputStream ois = ois = new ObjectInputStream(
            new BufferedInputStream(new FileInputStream(bloomFile)));
    BloomFilter filter = (BloomFilter) ois.readObject();
    ois.close();

    printStats(filter, System.out);

    BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));
    String line;
    CodonWalker walker = null;
    while ((line = reader.readLine()) != null) {
        char[] kmer = line.toCharArray();
        System.out.print(line + "\t");
        try {
            walker = filter.new RightCodonFacade(kmer);
            walker.jumpTo(kmer);
            System.out.print("present");
        } catch (Exception e) {
            System.out.print("not present\t" + e.getMessage());
        }
        System.out.println();
    }
}