Example usage for java.io BufferedReader BufferedReader

List of usage examples for java.io BufferedReader BufferedReader

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Introduction

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

Prototype

public BufferedReader(Reader in)

Source Link

Document

Creates a buffering character-input stream that uses a default-sized input buffer.

Usage

From source file:edu.umd.shrawanraina.SequentialPersonalizedPageRank.java

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

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    options.addOption(//from w w w  .  j  a  v  a  2s  . c  om
            OptionBuilder.withArgName("val").hasArg().withDescription("random jump factor").create(JUMP));
    options.addOption(OptionBuilder.withArgName("node").hasArg()
            .withDescription("source node (i.e., destination of the random jump)").create(SOURCE));

    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(INPUT) || !cmdline.hasOption(SOURCE)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(SequentialPersonalizedPageRank.class.getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        System.exit(-1);
    }

    String infile = cmdline.getOptionValue(INPUT);
    final String source = cmdline.getOptionValue(SOURCE);
    float alpha = cmdline.hasOption(JUMP) ? Float.parseFloat(cmdline.getOptionValue(JUMP)) : 0.15f;

    int edgeCnt = 0;
    DirectedSparseGraph<String, Integer> graph = new DirectedSparseGraph<String, Integer>();

    BufferedReader data = new BufferedReader(new InputStreamReader(new FileInputStream(infile)));

    String line;
    while ((line = data.readLine()) != null) {
        line.trim();
        String[] arr = line.split("\\t");

        for (int i = 1; i < arr.length; i++) {
            graph.addEdge(new Integer(edgeCnt++), arr[0], arr[i]);
        }
    }

    data.close();

    if (!graph.containsVertex(source)) {
        System.err.println("Error: source node not found in the graph!");
        System.exit(-1);
    }

    WeakComponentClusterer<String, Integer> clusterer = new WeakComponentClusterer<String, Integer>();

    Set<Set<String>> components = clusterer.transform(graph);
    int numComponents = components.size();
    System.out.println("Number of components: " + numComponents);
    System.out.println("Number of edges: " + graph.getEdgeCount());
    System.out.println("Number of nodes: " + graph.getVertexCount());
    System.out.println("Random jump factor: " + alpha);

    // Compute personalized PageRank.
    PageRankWithPriors<String, Integer> ranker = new PageRankWithPriors<String, Integer>(graph,
            new Transformer<String, Double>() {
                public Double transform(String vertex) {
                    return vertex.equals(source) ? 1.0 : 0;
                }
            }, alpha);

    ranker.evaluate();

    // Use priority queue to sort vertices by PageRank values.
    PriorityQueue<Ranking<String>> q = new PriorityQueue<Ranking<String>>();
    int i = 0;
    for (String pmid : graph.getVertices()) {
        q.add(new Ranking<String>(i++, ranker.getVertexScore(pmid), pmid));
    }

    // Print PageRank values.
    System.out.println("\nPageRank of nodes, in descending order:");
    Ranking<String> r = null;
    while ((r = q.poll()) != null) {
        System.out.println(r.rankScore + "\t" + r.getRanked());
    }
}

From source file:edu.umd.ujjwalgoel.AnalyzePMI.java

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

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));

    CommandLine cmdline = null;/*  w  w  w  .jav  a  2s .com*/
    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(INPUT)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(AnalyzePMI.class.getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        System.exit(-1);
    }

    String inputPath = cmdline.getOptionValue(INPUT);
    System.out.println("input path: " + inputPath);

    BufferedReader br = null;
    int countPairs = 0;

    List<PairOfWritables<PairOfStrings, FloatWritable>> pmis = new ArrayList<PairOfWritables<PairOfStrings, FloatWritable>>();
    List<PairOfWritables<PairOfStrings, FloatWritable>> cloudPmis = new ArrayList<PairOfWritables<PairOfStrings, FloatWritable>>();
    List<PairOfWritables<PairOfStrings, FloatWritable>> lovePmis = new ArrayList<PairOfWritables<PairOfStrings, FloatWritable>>();

    PairOfWritables<PairOfStrings, FloatWritable> highestPMI = null;
    PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI = null;
    PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI2 = null;
    PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI3 = null;

    PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI = null;
    PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI2 = null;
    PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI3 = null;

    try {
        FileSystem fs = FileSystem.get(new Configuration());
        FileStatus[] status = fs.listStatus(new Path(inputPath));
        //PairOfStrings pair = new PairOfStrings();
        for (int i = 0; i < status.length; i++) {
            br = new BufferedReader(new InputStreamReader(fs.open(status[i].getPath())));
            String line = br.readLine();
            while (line != null) {
                String[] words = line.split("\\t");
                float value = Float.parseFloat(words[1].trim());
                String[] wordPair = words[0].replaceAll("\\(", "").replaceAll("\\)", "").split(",");
                PairOfStrings pair = new PairOfStrings();
                pair.set(wordPair[0].trim(), wordPair[1].trim());
                if (wordPair[0].trim().equals("cloud")) {
                    PairOfWritables<PairOfStrings, FloatWritable> cloudPmi = new PairOfWritables<PairOfStrings, FloatWritable>();
                    cloudPmi.set(pair, new FloatWritable(value));
                    cloudPmis.add(cloudPmi);
                    if ((highestCloudPMI == null)
                            || (highestCloudPMI.getRightElement().compareTo(cloudPmi.getRightElement()) < 0)) {
                        highestCloudPMI = cloudPmi;
                    } else if ((highestCloudPMI2 == null)
                            || (highestCloudPMI2.getRightElement().compareTo(cloudPmi.getRightElement()) < 0)) {
                        highestCloudPMI2 = cloudPmi;
                    } else if ((highestCloudPMI3 == null)
                            || (highestCloudPMI3.getRightElement().compareTo(cloudPmi.getRightElement()) < 0)) {
                        highestCloudPMI3 = cloudPmi;
                    }
                }
                if (wordPair[0].trim().equals("love")) {
                    PairOfWritables<PairOfStrings, FloatWritable> lovePmi = new PairOfWritables<PairOfStrings, FloatWritable>();
                    lovePmi.set(pair, new FloatWritable(value));
                    lovePmis.add(lovePmi);
                    if ((highestLovePMI == null)
                            || (highestLovePMI.getRightElement().compareTo(lovePmi.getRightElement()) < 0)) {
                        highestLovePMI = lovePmi;
                    } else if ((highestLovePMI2 == null)
                            || (highestLovePMI2.getRightElement().compareTo(lovePmi.getRightElement()) < 0)) {
                        highestLovePMI2 = lovePmi;
                    } else if ((highestLovePMI3 == null)
                            || (highestLovePMI3.getRightElement().compareTo(lovePmi.getRightElement()) < 0)) {
                        highestLovePMI3 = lovePmi;
                    }
                }
                PairOfWritables<PairOfStrings, FloatWritable> pmi = new PairOfWritables<PairOfStrings, FloatWritable>();
                pmi.set(pair, new FloatWritable(value));
                pmis.add(pmi);
                if (highestPMI == null) {
                    highestPMI = pmi;
                } else if (highestPMI.getRightElement().compareTo(pmi.getRightElement()) < 0) {
                    highestPMI = pmi;
                }
                countPairs++;
                line = br.readLine();
            }
        }
    } catch (Exception ex) {
        System.out.println("ERROR" + ex.getMessage());
    }

    /*Collections.sort(pmis, new Comparator<PairOfWritables<PairOfStrings, FloatWritable>>() {
      public int compare(PairOfWritables<PairOfStrings, FloatWritable> e1,
          PairOfWritables<PairOfStrings, FloatWritable> e2) {
        /*if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
          return e1.getLeftElement().getLeftElement().compareTo(e2.getLeftElement().getLeftElement());
        }
            
        return e2.getRightElement().compareTo(e1.getRightElement());
      }
    });
            
            
    Collections.sort(cloudPmis, new Comparator<PairOfWritables<PairOfStrings, FloatWritable>>() {
      public int compare(PairOfWritables<PairOfStrings, FloatWritable> e1,
          PairOfWritables<PairOfStrings, FloatWritable> e2) {
        if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
    return e1.getLeftElement().getLeftElement().compareTo(e2.getLeftElement().getLeftElement());
            }
            
        return e2.getRightElement().compareTo(e1.getRightElement());
      }
    });
            
            
    Collections.sort(lovePmis, new Comparator<PairOfWritables<PairOfStrings, FloatWritable>>() {
      public int compare(PairOfWritables<PairOfStrings, FloatWritable> e1,
          PairOfWritables<PairOfStrings, FloatWritable> e2) {
        if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
    return e1.getLeftElement().getLeftElement().compareTo(e2.getLeftElement().getLeftElement());
           }
            
        return e2.getRightElement().compareTo(e1.getRightElement());
      }
    });
            
     PairOfWritables<PairOfStrings, FloatWritable> highestPMI = pmis.get(0);
     PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI = cloudPmis.get(0);      PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI2 = cloudPmis.get(1);
     PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI3 = cloudPmis.get(2);
             
     PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI = lovePmis.get(0);       PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI2 = lovePmis.get(1);
     PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI3 = lovePmis.get(2);*/

    System.out.println("Total Distinct Pairs : " + countPairs);
    System.out.println("Pair with highest PMI : (" + highestPMI.getLeftElement().getLeftElement() + ", "
            + highestPMI.getLeftElement().getRightElement());

    System.out
            .println("Word with highest PMI with Cloud : " + highestCloudPMI.getLeftElement().getRightElement()
                    + " with value : " + highestCloudPMI.getRightElement().get());
    System.out.println(
            "Word with second highest PMI with Cloud : " + highestCloudPMI2.getLeftElement().getRightElement()
                    + " with value : " + highestCloudPMI2.getRightElement().get());
    System.out.println(
            "Word with third highest PMI with Cloud : " + highestCloudPMI3.getLeftElement().getRightElement()
                    + " with value : " + highestCloudPMI3.getRightElement().get());

    System.out.println("Word with highest PMI with Love : " + highestLovePMI.getLeftElement().getRightElement()
            + " with value : " + highestLovePMI.getRightElement().get());
    System.out.println(
            "Word with second highest PMI with Love : " + highestLovePMI2.getLeftElement().getRightElement()
                    + " with value : " + highestLovePMI2.getRightElement().get());
    System.out.println(
            "Word with third highest PMI with Love : " + highestLovePMI3.getLeftElement().getRightElement()
                    + " with value : " + highestLovePMI3.getRightElement().get());

}

From source file:examples.mail.IMAPImportMbox.java

public static void main(String[] args) throws IOException {
    if (args.length < 2) {
        System.err.println(//from www  . j a  va  2s .co m
                "Usage: IMAPImportMbox imap[s]://user:password@host[:port]/folder/path <mboxfile> [selectors]");
        System.err.println("\tWhere: a selector is a list of numbers/number ranges - 1,2,3-10"
                + " - or a list of strings to match in the initial From line");
        System.exit(1);
    }

    final URI uri = URI.create(args[0]);
    final String file = args[1];

    final File mbox = new File(file);
    if (!mbox.isFile() || !mbox.canRead()) {
        throw new IOException("Cannot read mailbox file: " + mbox);
    }

    String path = uri.getPath();
    if (path == null || path.length() < 1) {
        throw new IllegalArgumentException("Invalid folderPath: '" + path + "'");
    }
    String folder = path.substring(1); // skip the leading /

    List<String> contains = new ArrayList<String>(); // list of strings to find
    BitSet msgNums = new BitSet(); // list of message numbers

    for (int i = 2; i < args.length; i++) {
        String arg = args[i];
        if (arg.matches("\\d+(-\\d+)?(,\\d+(-\\d+)?)*")) { // number,m-n
            for (String entry : arg.split(",")) {
                String[] parts = entry.split("-");
                if (parts.length == 2) { // m-n
                    int low = Integer.parseInt(parts[0]);
                    int high = Integer.parseInt(parts[1]);
                    for (int j = low; j <= high; j++) {
                        msgNums.set(j);
                    }
                } else {
                    msgNums.set(Integer.parseInt(entry));
                }
            }
        } else {
            contains.add(arg); // not a number/number range
        }
    }
    //        System.out.println(msgNums.toString());
    //        System.out.println(java.util.Arrays.toString(contains.toArray()));

    // Connect and login
    final IMAPClient imap = IMAPUtils.imapLogin(uri, 10000, null);

    int total = 0;
    int loaded = 0;
    try {
        imap.setSoTimeout(6000);

        final BufferedReader br = new BufferedReader(new FileReader(file)); // TODO charset?

        String line;
        StringBuilder sb = new StringBuilder();
        boolean wanted = false; // Skip any leading rubbish
        while ((line = br.readLine()) != null) {
            if (line.startsWith("From ")) { // start of message; i.e. end of previous (if any)
                if (process(sb, imap, folder, total)) { // process previous message (if any)
                    loaded++;
                }
                sb.setLength(0);
                total++;
                wanted = wanted(total, line, msgNums, contains);
            } else if (startsWith(line, PATFROM)) { // Unescape ">+From " in body text
                line = line.substring(1);
            }
            // TODO process first Received: line to determine arrival date?
            if (wanted) {
                sb.append(line);
                sb.append(CRLF);
            }
        }
        br.close();
        if (wanted && process(sb, imap, folder, total)) { // last message (if any)
            loaded++;
        }
    } catch (IOException e) {
        System.out.println(imap.getReplyString());
        e.printStackTrace();
        System.exit(10);
        return;
    } finally {
        imap.logout();
        imap.disconnect();
    }
    System.out.println("Processed " + total + " messages, loaded " + loaded);
}

From source file:DruidResponseTime.java

public static void main(String[] args) throws Exception {
    try (CloseableHttpClient client = HttpClients.createDefault()) {
        HttpPost post = new HttpPost("http://localhost:8082/druid/v2/?pretty");
        post.addHeader("content-type", "application/json");
        CloseableHttpResponse res;//ww  w. j  a  v a 2 s . c  om

        if (STORE_RESULT) {
            File dir = new File(RESULT_DIR);
            if (!dir.exists()) {
                dir.mkdirs();
            }
        }

        int length;

        // Make sure all segments online
        System.out.println("Test if number of records is " + RECORD_NUMBER);
        post.setEntity(new StringEntity("{" + "\"queryType\":\"timeseries\","
                + "\"dataSource\":\"tpch_lineitem\"," + "\"intervals\":[\"1992-01-01/1999-01-01\"],"
                + "\"granularity\":\"all\"," + "\"aggregations\":[{\"type\":\"count\",\"name\":\"count\"}]}"));
        while (true) {
            System.out.print('*');
            res = client.execute(post);
            boolean valid;
            try (BufferedInputStream in = new BufferedInputStream(res.getEntity().getContent())) {
                length = in.read(BYTE_BUFFER);
                valid = new String(BYTE_BUFFER, 0, length, "UTF-8").contains("\"count\" : 6001215");
            }
            res.close();
            if (valid) {
                break;
            } else {
                Thread.sleep(5000);
            }
        }
        System.out.println("Number of Records Test Passed");

        for (int i = 0; i < QUERIES.length; i++) {
            System.out.println(
                    "--------------------------------------------------------------------------------");
            System.out.println("Start running query: " + QUERIES[i]);
            try (BufferedReader reader = new BufferedReader(
                    new FileReader(QUERY_FILE_DIR + File.separator + i + ".json"))) {
                length = reader.read(CHAR_BUFFER);
                post.setEntity(new StringEntity(new String(CHAR_BUFFER, 0, length)));
            }

            // Warm-up Rounds
            System.out.println("Run " + WARMUP_ROUND + " times to warm up cache...");
            for (int j = 0; j < WARMUP_ROUND; j++) {
                res = client.execute(post);
                res.close();
                System.out.print('*');
            }
            System.out.println();

            // Test Rounds
            int[] time = new int[TEST_ROUND];
            int totalTime = 0;
            System.out.println("Run " + TEST_ROUND + " times to get average time...");
            for (int j = 0; j < TEST_ROUND; j++) {
                long startTime = System.currentTimeMillis();
                res = client.execute(post);
                long endTime = System.currentTimeMillis();
                if (STORE_RESULT && j == 0) {
                    try (BufferedInputStream in = new BufferedInputStream(res.getEntity().getContent());
                            BufferedWriter writer = new BufferedWriter(
                                    new FileWriter(RESULT_DIR + File.separator + i + ".json", false))) {
                        while ((length = in.read(BYTE_BUFFER)) > 0) {
                            writer.write(new String(BYTE_BUFFER, 0, length, "UTF-8"));
                        }
                    }
                }
                res.close();
                time[j] = (int) (endTime - startTime);
                totalTime += time[j];
                System.out.print(time[j] + "ms ");
            }
            System.out.println();

            // Process Results
            double avgTime = (double) totalTime / TEST_ROUND;
            double stdDev = 0;
            for (int temp : time) {
                stdDev += (temp - avgTime) * (temp - avgTime) / TEST_ROUND;
            }
            stdDev = Math.sqrt(stdDev);
            System.out.println("The average response time for the query is: " + avgTime + "ms");
            System.out.println("The standard deviation is: " + stdDev);
        }
    }
}

From source file:com.aestel.chemistry.openEye.fp.apps.SDFFPNNFinder.java

public static void main(String... args) throws IOException {
    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;/*from   ww  w.ja v  a2s.c om*/
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        exitWithHelp();
    }

    args = cmd.getArgs();
    if (args.length > 0) {
        exitWithHelp("Unknown param: " + args[0]);
    }

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

    int nCpu = 1;
    int maxNeighbors = 1;
    double minSim = 0D;

    String fpTag = cmd.getOptionValue("fpTag");
    String idTag = cmd.getOptionValue("idTag");
    boolean doMaxTanimoto = cmd.hasOption("maxTanimoto");
    boolean printAll = cmd.hasOption("printAll");

    String d = cmd.getOptionValue("nCpu");
    if (d != null)
        nCpu = Integer.parseInt(d);

    d = cmd.getOptionValue("maxNeighbors");
    if (d != null)
        maxNeighbors = Integer.parseInt(d);

    d = cmd.getOptionValue("minSimilarity");
    if (d != null)
        minSim = Double.parseDouble(d);

    String countAboveSimilarityStr = cmd.getOptionValue("countSimilarAbove");

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    String refFile = cmd.getOptionValue("ref");

    String tabOutput = cmd.getOptionValue("tabOutput");
    boolean outputDuplicates = cmd.hasOption("outputDuplicates");

    if (outputDuplicates && tabOutput != null)
        exitWithHelp("-outputDuplicates will not work with tabOutput");

    if (outputDuplicates && refFile == null)
        exitWithHelp("-outputDuplicates requires -ref ");

    if ("tab".equalsIgnoreCase(tabOutput) && refFile != null)
        exitWithHelp("-tabOutput tab: does not work with reference file");

    if ("tab".equalsIgnoreCase(tabOutput) && maxNeighbors == 1)
        exitWithHelp("-tabOutput tab: does not make sense with -maxNeighbors = 1");

    if (cmd.hasOption("countSimilarAbove") && tabOutput != null)
        exitWithHelp("-countSimilarAbove not supported for tab or vTab output");

    if (printAll && !(maxNeighbors > 1 || minSim > 0))
        exitWithHelp("printAll only supported if: maxNeighbors > 1 or minSim > 0");

    if (printAll && tabOutput != null)
        System.err.println("WARNING: printAll ignored tor tab output!\n");

    SimComparatorFactory<OEMolBase, FPComparator, FPComparator> compFact = new FPComparatorFact(doMaxTanimoto,
            fpTag);

    if (refFile == null) {
        perfromMatrixNNSearch(inFile, outFile, tabOutput, compFact, minSim, maxNeighbors, idTag, nCpu,
                countAboveSimilarityStr, printAll);

    } else {
        performReferenceSearch(inFile, refFile, outFile, tabOutput, compFact, minSim, maxNeighbors, idTag, nCpu,
                countAboveSimilarityStr, outputDuplicates, printAll);
    }

}

From source file:edu.wisc.doit.tcrypt.cli.TokenCrypt.java

public static void main(String[] args) throws IOException {
    // create Options object
    final Options options = new Options();

    // operation opt group
    final OptionGroup cryptTypeGroup = new OptionGroup();
    cryptTypeGroup.addOption(new Option("e", "encrypt", false, "Encrypt a token"));
    cryptTypeGroup.addOption(new Option("d", "decrypt", false, "Decrypt a token"));
    cryptTypeGroup/*w  w w.  j  ava 2  s.  co  m*/
            .addOption(new Option("c", "check", false, "Check if the string looks like an encrypted token"));
    cryptTypeGroup.setRequired(true);
    options.addOptionGroup(cryptTypeGroup);

    // token source opt group
    final OptionGroup tokenGroup = new OptionGroup();
    final Option tokenOpt = new Option("t", "token", true, "The token(s) to operate on");
    tokenOpt.setArgs(Option.UNLIMITED_VALUES);
    tokenGroup.addOption(tokenOpt);
    final Option tokenFileOpt = new Option("f", "file", true,
            "A file with one token per line to operate on, if - is specified stdin is used");
    tokenGroup.addOption(tokenFileOpt);
    tokenGroup.setRequired(true);
    options.addOptionGroup(tokenGroup);

    final Option keyOpt = new Option("k", "keyFile", true,
            "Key file to use. Must be a private key for decryption and a public key for encryption");
    keyOpt.setRequired(true);
    options.addOption(keyOpt);

    // create the parser
    final CommandLineParser parser = new GnuParser();
    CommandLine line = null;
    try {
        // parse the command line arguments
        line = parser.parse(options, args);
    } catch (ParseException exp) {
        // automatically generate the help statement
        System.err.println(exp.getMessage());
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java " + TokenCrypt.class.getName(), options, true);
        System.exit(1);
    }

    final Reader keyReader = createKeyReader(line);

    final TokenHandler tokenHandler = createTokenHandler(line, keyReader);

    if (line.hasOption("t")) {
        //tokens on cli
        final String[] tokens = line.getOptionValues("t");
        for (final String token : tokens) {
            handleToken(tokenHandler, token);
        }
    } else {
        //tokens from a file
        final String tokenFile = line.getOptionValue("f");
        final BufferedReader fileReader;
        if ("-".equals(tokenFile)) {
            fileReader = new BufferedReader(new InputStreamReader(System.in));
        } else {
            fileReader = new BufferedReader(new FileReader(tokenFile));
        }

        while (true) {
            final String token = fileReader.readLine();
            if (token == null) {
                break;
            }

            handleToken(tokenHandler, token);
        }
    }
}

From source file:com.genentech.chemistry.openEye.apps.SDFRingSystemExtractor.java

/**
 * @param args/*  ww w  .j  a  v  a 2 s . com*/
 */
public static void main(String... args) throws IOException { // create command line Options object
    Options options = new Options();
    Option opt = new Option(OPT_INFILE, true, "input file oe-supported");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_OUTFILE, true, "output file oe-supported");
    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();
    }

    String inFile = cmd.getOptionValue(OPT_INFILE);
    String outFile = cmd.getOptionValue(OPT_OUTFILE);
    SDFRingSystemExtractor extractor = new SDFRingSystemExtractor(outFile);
    extractor.run(inFile);
    extractor.close();
}

From source file:test.TestJavaService.java

/**
 * Main.  The cmdline arguments either do or don't contain the flag -remote: that's the only supported flag.  If it is specified,
 *   we test code on the AWS instance.  If it is not, we test code running locally.
 * The first non-flag argument is the "verb", which (currently) should be one of the verbs set at the top of source file
 *   org.qcert.javasrc.Main.  Remaining non-flag arguments are file names.  There must be at least one.  The number of such 
 *   arguments and what they should contain depends on the verb.
 * @throws Exception// w  w  w  .java2  s . com
 */
public static void main(String[] args) throws Exception {
    /* Parse command line */
    List<String> files = new ArrayList<>();
    String loc = "localhost", verb = null;
    for (String arg : args) {
        if (arg.equals("-remote"))
            loc = REMOTE_LOC;
        else if (arg.startsWith("-"))
            illegal();
        else if (verb == null)
            verb = arg;
        else
            files.add(arg);
    }
    /* Simple consistency checks and verb-specific parsing */
    if (files.size() == 0)
        illegal();
    String file = files.remove(0);
    String schema = null;
    switch (verb) {
    case "parseSQL":
    case "serialRule2CAMP":
    case "sqlSchema2JSON":
        if (files.size() != 0)
            illegal();
        break;
    case "techRule2CAMP":
        if (files.size() != 1)
            illegal();
        schema = files.get(0);
        break;
    case "csv2JSON":
        if (files.size() < 1)
            illegal();
        break;
    default:
        illegal();
    }

    /* Assemble information from arguments */
    String url = String.format("http://%s:9879?verb=%s", loc, verb);
    byte[] contents = Files.readAllBytes(Paths.get(file));
    String toSend;
    if ("serialRule2CAMP".equals(verb))
        toSend = Base64.getEncoder().encodeToString(contents);
    else
        toSend = new String(contents);
    if ("techRule2CAMP".equals(verb))
        toSend = makeSpecialJson(toSend, schema);
    else if ("csv2JSON".equals(verb))
        toSend = makeSpecialJson(toSend, files);
    HttpClient client = HttpClients.createDefault();
    HttpPost post = new HttpPost(url);
    StringEntity entity = new StringEntity(toSend);
    entity.setContentType("text/plain");
    post.setEntity(entity);
    HttpResponse resp = client.execute(post);
    int code = resp.getStatusLine().getStatusCode();
    if (code == HttpStatus.SC_OK) {
        HttpEntity answer = resp.getEntity();
        InputStream s = answer.getContent();
        BufferedReader rdr = new BufferedReader(new InputStreamReader(s));
        String line = rdr.readLine();
        while (line != null) {
            System.out.println(line);
            line = rdr.readLine();
        }
        rdr.close();
        s.close();
    } else
        System.out.println(resp.getStatusLine());
}

From source file:EchoClient.java

 public static void main(String[] args) throws IOException {

   ServerSocket serverSocket = null;
   try {//from  w  ww.  j a  v  a 2s .c  om
      serverSocket = new ServerSocket(4444);
   } catch (IOException e) {
      System.err.println("Could not listen on port: 4444.");
      System.exit(1);
   }

   Socket clientSocket = null;
   try {
      clientSocket = serverSocket.accept();
   } catch (IOException e) {
      System.err.println("Accept failed.");
      System.exit(1);
   }

   PrintWriter out = new PrintWriter(clientSocket.getOutputStream(), true);
   BufferedReader in = new BufferedReader(new InputStreamReader(
         clientSocket.getInputStream()));
   String inputLine, outputLine;
   KnockKnockProtocol kkp = new KnockKnockProtocol();

   outputLine = kkp.processInput(null);
   out.println(outputLine);

   while ((inputLine = in.readLine()) != null) {
      outputLine = kkp.processInput(inputLine);
      out.println(outputLine);
      if (outputLine.equals("Bye."))
         break;
   }
   out.close();
   in.close();
   clientSocket.close();
   serverSocket.close();
}

From source file:com.act.lcms.MassCalculator2.java

public static void main(String[] args) throws Exception {
    CommandLine cl = CLI_UTIL.parseCommandLine(args);

    if (cl.hasOption(OPTION_LICENSE_FILE)) {
        LOGGER.info("Using license file at %s", cl.getOptionValue(OPTION_LICENSE_FILE));
        LicenseManager.setLicenseFile(cl.getOptionValue(OPTION_LICENSE_FILE));
    }/* w ww .jav  a 2 s .c om*/

    List<String> inchis = new ArrayList<>();

    if (cl.hasOption(OPTION_INPUT_FILE)) {
        try (BufferedReader reader = new BufferedReader(new FileReader(cl.getOptionValue(OPTION_INPUT_FILE)))) {
            String line;
            while ((line = reader.readLine()) != null) {
                inchis.add(line);
            }
        }
    }

    if (cl.getArgList().size() > 0) {
        LOGGER.info("Reading %d InChIs from the command line", cl.getArgList().size());
        inchis.addAll(cl.getArgList());
    }

    try (PrintWriter writer = new PrintWriter(
            cl.hasOption(OPTION_OUTPUT_FILE) ? new FileWriter(cl.getOptionValue(OPTION_OUTPUT_FILE))
                    : new OutputStreamWriter(System.out))) {
        writer.format("InChI\tMass\tCharge\n");

        for (String inchi : inchis) {
            try {
                Pair<Double, Integer> massAndCharge = calculateMassAndCharge(inchi);
                writer.format("%s\t%.6f\t%3d\n", inchi, massAndCharge.getLeft(), massAndCharge.getRight());
            } catch (MolFormatException e) {
                LOGGER.error("Unable to compute mass for %s: %s", inchi, e.getMessage());
            }
        }
    }
}