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:com.bitsofproof.example.Simple.java

public static void main(String[] args) {
    Security.addProvider(new BouncyCastleProvider());

    final CommandLineParser parser = new GnuParser();
    final Options gnuOptions = new Options();
    gnuOptions.addOption("h", "help", false, "I can't help you yet");
    gnuOptions.addOption("s", "server", true, "Server URL");
    gnuOptions.addOption("u", "user", true, "User");
    gnuOptions.addOption("p", "password", true, "Password");

    System.out.println("BOP Bitcoin Server Simple Client 3.5.0 (c) 2013-2014 bits of proof zrt.");
    CommandLine cl = null;/*www  .  j a v a2  s.  com*/
    String url = null;
    String user = null;
    String password = null;
    try {
        cl = parser.parse(gnuOptions, args);
        url = cl.getOptionValue('s');
        user = cl.getOptionValue('u');
        password = cl.getOptionValue('p');
    } catch (org.apache.commons.cli.ParseException e) {
        e.printStackTrace();
        System.exit(1);
    }
    if (url == null || user == null || password == null) {
        System.err.println("Need -s server -u user -p password");
        System.exit(1);
    }

    BCSAPI api = getServer(url, user, password);
    try {
        BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
        long start = System.currentTimeMillis();
        api.ping(start);
        System.out.println("Server round trip " + (System.currentTimeMillis() - start) + "ms");
        api.addAlertListener(new AlertListener() {
            @Override
            public void alert(String s, int severity) {
                System.err.println("ALERT: " + s);
            }
        });
        System.out.println("Talking to " + (api.isProduction() ? "PRODUCTION" : "test") + " server");
        ConfirmationManager confirmationManager = new ConfirmationManager();
        confirmationManager.init(api, 144);
        System.out.printf("Please enter wallet name: ");
        String wallet = input.readLine();
        SimpleFileWallet w = new SimpleFileWallet(wallet + ".wallet");
        TransactionFactory am = null;
        if (!w.exists()) {
            System.out.printf("Enter passphrase: ");
            String passphrase = input.readLine();
            System.out.printf("Enter master (empty for new): ");
            String master = input.readLine();
            if (master.equals("")) {
                w.init(passphrase);
                w.unlock(passphrase);
                System.out.printf("First account: ");
                String account = input.readLine();
                am = w.createAccountManager(account);
                w.lock();
                w.persist();
            } else {
                StringTokenizer tokenizer = new StringTokenizer(master, "@");
                String key = tokenizer.nextToken();
                long since = 0;
                if (tokenizer.hasMoreElements()) {
                    since = Long.parseLong(tokenizer.nextToken()) * 1000;
                }
                w.init(passphrase, ExtendedKey.parse(key), true, since);
                w.unlock(passphrase);
                System.out.printf("First account: ");
                String account = input.readLine();
                am = w.createAccountManager(account);
                w.lock();
                w.persist();
                w.sync(api);
            }
        } else {
            w = SimpleFileWallet.read(wallet + ".wallet");
            w.sync(api);
            List<String> names = w.getAccountNames();
            System.out.println("Accounts:");
            System.out.println("---------");
            String first = null;
            for (String name : names) {
                System.out.println(name);
                if (first == null) {
                    first = name;
                }
            }
            System.out.println("---------");
            am = w.getAccountManager(first);
            System.out.println("Using account " + first);
        }
        confirmationManager.addAccount(am);
        api.registerTransactionListener(am);

        while (true) {
            printMenu();
            String answer = input.readLine();
            System.out.printf("\n");
            if (answer.equals("1")) {
                System.out.printf("The balance is: " + printBit(am.getBalance()) + "\n");
                System.out.printf("     confirmed: " + printBit(am.getConfirmed()) + "\n");
                System.out.printf("    receiveing: " + printBit(am.getReceiving()) + "\n");
                System.out.printf("        change: " + printBit(am.getChange()) + "\n");
                System.out.printf("(      sending: " + printBit(am.getSending()) + ")\n");
            } else if (answer.equals("2")) {
                for (Address a : am.getAddresses()) {
                    System.out.printf(a + "\n");
                }
            } else if (answer.equals("3")) {
                ExtendedKeyAccountManager im = (ExtendedKeyAccountManager) am;
                System.out.printf(
                        im.getMaster().serialize(api.isProduction()) + "@" + im.getCreated() / 1000 + "\n");
            } else if (answer.equals("4")) {
                System.out.printf("Enter passphrase: ");
                String passphrase = input.readLine();
                w.unlock(passphrase);
                ExtendedKeyAccountManager im = (ExtendedKeyAccountManager) am;
                System.out.printf(
                        im.getMaster().serialize(api.isProduction()) + "@" + im.getCreated() / 1000 + "\n");
                w.lock();
            } else if (answer.equals("5")) {
                System.out.printf("Enter passphrase: ");
                String passphrase = input.readLine();
                w.unlock(passphrase);
                System.out.printf("Number of recipients");
                Integer nr = Integer.valueOf(input.readLine());
                Transaction spend;
                if (nr.intValue() == 1) {
                    System.out.printf("Receiver address: ");
                    String address = input.readLine();
                    System.out.printf("amount (Bit): ");
                    long amount = parseBit(input.readLine());
                    spend = am.pay(Address.fromSatoshiStyle(address), amount);
                    System.out.println("About to send " + printBit(amount) + " to " + address);
                } else {
                    List<Address> addresses = new ArrayList<>();
                    List<Long> amounts = new ArrayList<>();
                    long total = 0;
                    for (int i = 0; i < nr; ++i) {
                        System.out.printf("Receiver address: ");
                        String address = input.readLine();
                        addresses.add(Address.fromSatoshiStyle(address));
                        System.out.printf("amount (Bit): ");
                        long amount = parseBit(input.readLine());
                        amounts.add(amount);
                        total += amount;
                    }
                    spend = am.pay(addresses, amounts);
                    System.out.println("About to send " + printBit(total));
                }
                System.out.println("inputs");
                for (TransactionInput in : spend.getInputs()) {
                    System.out.println(in.getSourceHash() + " " + in.getIx());
                }
                System.out.println("outputs");
                for (TransactionOutput out : spend.getOutputs()) {
                    System.out.println(out.getOutputAddress() + " " + printBit(out.getValue()));
                }
                w.lock();
                System.out.printf("Type yes to go: ");
                if (input.readLine().equals("yes")) {
                    api.sendTransaction(spend);
                    System.out.printf("Sent transaction: " + spend.getHash());
                } else {
                    System.out.printf("Nothing happened.");
                }
            } else if (answer.equals("6")) {
                System.out.printf("Address: ");
                Set<Address> match = new HashSet<Address>();
                match.add(Address.fromSatoshiStyle(input.readLine()));
                api.scanTransactionsForAddresses(match, 0, new TransactionListener() {
                    @Override
                    public boolean process(Transaction t) {
                        System.out.printf("Found transaction: " + t.getHash() + "\n");
                        return true;
                    }
                });
            } else if (answer.equals("7")) {
                System.out.printf("Public key: ");
                ExtendedKey ek = ExtendedKey.parse(input.readLine());
                api.scanTransactions(ek, 0, 10, 0, new TransactionListener() {
                    @Override
                    public boolean process(Transaction t) {
                        System.out.printf("Found transaction: " + t.getHash() + "\n");
                        return true;
                    }
                });
            } else if (answer.equals("a")) {
                System.out.printf("Enter account name: ");
                String account = input.readLine();
                am = w.getAccountManager(account);
                api.registerTransactionListener(am);
                confirmationManager.addAccount(am);
            } else if (answer.equals("c")) {
                System.out.printf("Enter account name: ");
                String account = input.readLine();
                System.out.printf("Enter passphrase: ");
                String passphrase = input.readLine();
                w.unlock(passphrase);
                am = w.createAccountManager(account);
                System.out.println("using account: " + account);
                w.lock();
                w.persist();
                api.registerTransactionListener(am);
                confirmationManager.addAccount(am);
            } else if (answer.equals("m")) {
                System.out.printf("Enter passphrase: ");
                String passphrase = input.readLine();
                w.unlock(passphrase);
                System.out.println(w.getMaster().serialize(api.isProduction()));
                System.out.println(w.getMaster().getReadOnly().serialize(true));
                w.lock();
            } else if (answer.equals("s")) {
                System.out.printf("Enter private key: ");
                String key = input.readLine();
                ECKeyPair k = ECKeyPair.parseWIF(key);
                KeyListAccountManager alm = new KeyListAccountManager();
                alm.addKey(k);
                alm.syncHistory(api);
                Address a = am.getNextReceiverAddress();
                Transaction t = alm.pay(a, alm.getBalance(), PaymentOptions.receiverPaysFee);
                System.out.println("About to sweep " + printBit(alm.getBalance()) + " to " + a);
                System.out.println("inputs");
                for (TransactionInput in : t.getInputs()) {
                    System.out.println(in.getSourceHash() + " " + in.getIx());
                }
                System.out.println("outputs");
                for (TransactionOutput out : t.getOutputs()) {
                    System.out.println(out.getOutputAddress() + " " + printBit(out.getValue()));
                }
                System.out.printf("Type yes to go: ");
                if (input.readLine().equals("yes")) {
                    api.sendTransaction(t);
                    System.out.printf("Sent transaction: " + t.getHash());
                } else {
                    System.out.printf("Nothing happened.");
                }
            } else {
                System.exit(0);
            }
        }
    } catch (Exception e) {
        System.err.println("Something went wrong");
        e.printStackTrace();
        System.exit(1);
    }
}

From source file:ch.epfl.leb.sass.commandline.CommandLineInterface.java

/**
 * Shows help, launches the interpreter and executes scripts according to input args.
 * @param args input arguments//from  ww w  .ja v  a  2 s . co m
 */
public static void main(String args[]) {
    // parse input arguments
    CommandLineParser parser = new DefaultParser();
    CommandLine line = null;
    try {
        line = parser.parse(options, args);
    } catch (ParseException ex) {
        System.err.println("Parsing of arguments failed. Reason: " + ex.getMessage());
        System.err.println("Use -help for usage.");
        System.exit(1);
    }

    // decide how do we make the interpreter available based on options
    Interpreter interpreter = null;
    // show help and exit
    if (line.hasOption("help")) {
        HelpFormatter helpFormatter = new HelpFormatter();
        helpFormatter.printHelp("java -jar <jar-name>", options, true);
        System.exit(0);
        // launch interpreter inside current terminal
    } else if (line.hasOption("interpreter")) {
        // assign in, out and err streams to the interpreter
        interpreter = new Interpreter(new InputStreamReader(System.in), System.out, System.err, true);
        interpreter.setShowResults(true);
        // if a script was given, execute it before giving access to user
        if (line.hasOption("script")) {
            try {
                interpreter.source(line.getOptionValue("script"));
            } catch (IOException ex) {
                Logger.getLogger(BeanShellConsole.class.getName()).log(Level.SEVERE,
                        "IOException while executing shell script.", ex);
            } catch (EvalError ex) {
                Logger.getLogger(BeanShellConsole.class.getName()).log(Level.SEVERE,
                        "EvalError while executing shell script.", ex);
            }
        }
        // give access to user
        new Thread(interpreter).start();
        // only execute script and exit
    } else if (line.hasOption("script")) {
        interpreter = new Interpreter();
        try {
            interpreter.source(line.getOptionValue("script"));
            System.exit(0);
        } catch (IOException ex) {
            Logger.getLogger(BeanShellConsole.class.getName()).log(Level.SEVERE,
                    "IOException while executing shell script.", ex);
            System.exit(1);
        } catch (EvalError ex) {
            Logger.getLogger(BeanShellConsole.class.getName()).log(Level.SEVERE,
                    "EvalError while executing shell script.", ex);
            System.exit(1);
        }

        // Launches the RPC server with the model contained in the file whose
        // filename was passed by argument.
    } else if (line.hasOption("rpc_server")) {

        IJPluginModel model = new IJPluginModel();
        File file = new File(line.getOptionValue("rpc_server"));
        try {
            FileInputStream stream = new FileInputStream(file);
            model = IJPluginModel.read(stream);
        } catch (FileNotFoundException ex) {
            System.out.println("Error: " + file.getName() + " not found.");
            System.exit(1);
        } catch (Exception ex) {
            ex.printStackTrace();
        }

        // Check whether a port number was specified.
        if (line.hasOption("port")) {
            try {
                port = Integer.valueOf(line.getOptionValue("port"));
                System.out.println("Using port: " + String.valueOf(port));
            } catch (java.lang.NumberFormatException ex) {
                System.out.println("Error: the port number argument is not a number.");
                System.exit(1);
            }
        } else {
            System.out.println("No port number provided. Using default port: " + String.valueOf(port));
        }

        RPCServer server = new RPCServer(model, port);

        System.out.println("Starting RPC server...");
        server.serve();

    } else if (line.hasOption("port") & !line.hasOption("rpc_server")) {
        System.out.println("Error: Port number provided without requesting the RPC server. Exiting...");
        System.exit(1);

        // if System.console() returns null, it means we were launched by
        // double-clicking the .jar, so launch own BeanShellConsole
        // if System.console() returns null, it means we were launched by
        // double-clicking the .jar, so launch own ConsoleFrame
    } else if (System.console() == null) {
        BeanShellConsole cframe = new BeanShellConsole("SASS BeanShell Prompt");
        interpreter = cframe.getInterpreter();
        cframe.setVisible(true);
        System.setOut(cframe.getInterpreter().getOut());
        System.setErr(cframe.getInterpreter().getErr());
        new Thread(cframe.getInterpreter()).start();
        // otherwise, show help
    } else {
        HelpFormatter helpFormatter = new HelpFormatter();
        helpFormatter.printHelp("java -jar <jar-name>", options, true);
        System.exit(0);
    }

    if (interpreter != null) {
        printWelcomeText(interpreter.getOut());
    }
}

From source file:com.yahoo.athenz.example.ztoken.HttpExampleClient.java

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

    // parse our command line to retrieve required input

    CommandLine cmd = parseCommandLine(args);

    String domainName = cmd.getOptionValue("domain");
    String serviceName = cmd.getOptionValue("service");
    String privateKeyPath = cmd.getOptionValue("pkey");
    String keyId = cmd.getOptionValue("keyid");
    String url = cmd.getOptionValue("url");
    String ztsUrl = cmd.getOptionValue("ztsurl");
    String providerDomain = cmd.getOptionValue("provider-domain");
    String providerRole = cmd.getOptionValue("provider-role");

    // we need to generate our principal credentials (ntoken). In
    // addition to the domain and service names, we need the
    // the service's private key and the key identifier - the
    // service with the corresponding public key must already be
    // registered in ZMS

    PrivateKey privateKey = Crypto.loadPrivateKey(new File(privateKeyPath));
    ServiceIdentityProvider identityProvider = new SimpleServiceIdentityProvider(domainName, serviceName,
            privateKey, keyId);//from www .  j a va2s .  c o m

    // now we need to retrieve a role token (ztoken) for accessing
    // the provider Athenz enabled service

    RoleToken roleToken = null;
    try (ZTSClient ztsClient = new ZTSClient(ztsUrl, domainName, serviceName, identityProvider)) {
        roleToken = ztsClient.getRoleToken(providerDomain, providerRole);
    }

    if (roleToken == null) {
        System.out.println(
                "Unable to retrieve role token for: " + providerRole + " in domain: " + providerDomain);
        System.exit(1);
    }

    URL obj = new URL(url);
    HttpURLConnection con = (HttpURLConnection) obj.openConnection();

    // set our Athenz credentials. The ZTSClient provides the header
    // name that we must use for authorization token while the role
    // token itself provides the token string (ztoken).

    System.out.println("Using RoleToken: " + roleToken.getToken());
    con.setRequestProperty(ZTSClient.getHeader(), roleToken.getToken());

    // now process our request

    int responseCode = con.getResponseCode();
    switch (responseCode) {
    case HttpURLConnection.HTTP_FORBIDDEN:
        System.out.println("Request was forbidden - not authorized: " + con.getResponseMessage());
        break;
    case HttpURLConnection.HTTP_OK:
        System.out.println("Successful response: ");
        try (BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()))) {
            String inputLine;
            while ((inputLine = in.readLine()) != null) {
                System.out.println(inputLine);
            }
        }
        break;
    default:
        System.out.println("Request failed - response status code: " + responseCode);
    }
}

From source file:com.kappaware.logtrawler.Main.java

@SuppressWarnings("static-access")
static public void main(String[] argv) throws Throwable {

    Config config;//from  w w  w  . j  a  v  a2 s .co m

    Options options = new Options();

    options.addOption(OptionBuilder.hasArg().withArgName("configFile").withLongOpt("config-file")
            .withDescription("JSON configuration file").create("c"));
    options.addOption(OptionBuilder.hasArg().withArgName("folder").withLongOpt("folder")
            .withDescription("Folder to monitor").create("f"));
    options.addOption(OptionBuilder.hasArg().withArgName("exclusion").withLongOpt("exclusion")
            .withDescription("Exclusion regex").create("x"));
    options.addOption(OptionBuilder.hasArg().withArgName("adminEndpoint").withLongOpt("admin-endpoint")
            .withDescription("Endpoint for admin REST").create("e"));
    options.addOption(OptionBuilder.hasArg().withArgName("outputFlow").withLongOpt("output-flow")
            .withDescription("Target to post result on").create("o"));
    options.addOption(OptionBuilder.hasArg().withArgName("hostname").withLongOpt("hostname")
            .withDescription("This hostname").create("h"));
    options.addOption(OptionBuilder.withLongOpt("displayDot").withDescription("Display Dot").create("d"));
    options.addOption(OptionBuilder.hasArg().withArgName("mimeType").withLongOpt("mime-type")
            .withDescription("Valid MIME type").create("m"));
    options.addOption(OptionBuilder.hasArg().withArgName("allowedAdmin").withLongOpt("allowedAdmin")
            .withDescription("Allowed admin network").create("a"));
    options.addOption(OptionBuilder.hasArg().withArgName("configFile").withLongOpt("gen-config-file")
            .withDescription("Generate JSON configuration file").create("g"));
    options.addOption(OptionBuilder.hasArg().withArgName("maxBatchSize").withLongOpt("max-batch-size")
            .withDescription("Max JSON batch (array) size").create("b"));

    CommandLineParser clParser = new BasicParser();
    CommandLine line;
    String configFile = null;
    try {
        // parse the command line argument
        line = clParser.parse(options, argv);
        if (line.hasOption("c")) {
            configFile = line.getOptionValue("c");
            config = Json.fromJson(Config.class,
                    new BufferedReader(new InputStreamReader(new FileInputStream(configFile))));
        } else {
            config = new Config();
        }
        if (line.hasOption("f")) {
            String[] fs = line.getOptionValues("f");
            // Get the first agent (Create it if needed)
            if (config.getAgents() == null || config.getAgents().size() == 0) {
                Config.Agent agent = new Config.Agent("default");
                config.addAgent(agent);
            }
            Config.Agent agent = config.getAgents().iterator().next();
            for (String f : fs) {
                agent.addFolder(new Config.Agent.Folder(f, false));
            }
        }
        if (line.hasOption("e")) {
            String e = line.getOptionValue("e");
            config.setAdminEndpoint(e);
        }
        if (line.hasOption("o")) {
            String[] es = line.getOptionValues("o");
            if (config.getAgents() != null) {
                for (Agent agent : config.getAgents()) {
                    for (String s : es) {
                        agent.addOuputFlow(s);
                    }
                }
            }
        }
        if (line.hasOption("h")) {
            String e = line.getOptionValue("h");
            config.setHostname(e);
        }
        if (line.hasOption("x")) {
            if (config.getAgents() != null) {
                for (Agent agent : config.getAgents()) {
                    if (agent.getFolders() != null) {
                        for (Folder folder : agent.getFolders()) {
                            String[] exs = line.getOptionValues("x");
                            for (String ex : exs) {
                                folder.addExcludedPath(ex);
                            }
                        }
                    }
                }
            }
        }
        if (line.hasOption("m")) {
            if (config.getAgents() != null) {
                for (Agent agent : config.getAgents()) {
                    String[] exs = line.getOptionValues("m");
                    for (String ex : exs) {
                        agent.addLogMimeType(ex);
                    }
                }
            }
        }
        if (line.hasOption("a")) {
            String[] exs = line.getOptionValues("a");
            for (String ex : exs) {
                config.addAdminAllowedNetwork(ex);
            }
        }
        if (line.hasOption("d")) {
            config.setDisplayDot(true);
        }
        if (line.hasOption("b")) {
            Integer i = getIntegerParameter(line, "b");
            if (config.getAgents() != null) {
                for (Agent agent : config.getAgents()) {
                    agent.setOutputMaxBatchSize(i);
                }
            }
        }
        config.setDefault();
        if (line.hasOption("g")) {
            String fileName = line.getOptionValue("g");
            PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(fileName, false)));
            out.println(Json.toJson(config, true));
            out.flush();
            out.close();
            System.exit(0);
        }
    } catch (ParseException exp) {
        // oops, something went wrong
        usage(options, exp.getMessage());
        return;
    }

    try {
        // Check config
        if (config.getAgents() == null || config.getAgents().size() < 1) {
            throw new ConfigurationException("At least one folder to monitor must be provided!");
        }
        Map<String, AgentHandler> agentHandlerByName = new HashMap<String, AgentHandler>();
        for (Config.Agent agent : config.getAgents()) {
            agentHandlerByName.put(agent.getName(), new AgentHandler(agent));
        }
        if (!Utils.isNullOrEmpty(config.getAdminEndpoint())) {
            new AdminServer(config, agentHandlerByName);
        }
    } catch (ConfigurationException e) {
        log.error(e.toString());
        System.exit(1);
    } catch (Throwable t) {
        log.error("Error in main", t);
        System.exit(2);
    }
}

From source file:com.dlmu.heipacker.crawler.client.ClientInteractiveAuthentication.java

public static void main(String[] args) throws Exception {
    DefaultHttpClient httpclient = new DefaultHttpClient();
    try {//from w ww . j a  v a2  s  . c  om
        // Create local execution context
        HttpContext localContext = new BasicHttpContext();

        HttpGet httpget = new HttpGet("http://localhost/test");

        boolean trying = true;
        while (trying) {
            System.out.println("executing request " + httpget.getRequestLine());
            HttpResponse response = httpclient.execute(httpget, localContext);

            System.out.println("----------------------------------------");
            System.out.println(response.getStatusLine());

            // Consume response content
            HttpEntity entity = response.getEntity();
            EntityUtils.consume(entity);

            int sc = response.getStatusLine().getStatusCode();

            AuthState authState = null;
            HttpHost authhost = null;
            if (sc == HttpStatus.SC_UNAUTHORIZED) {
                // Target host authentication required
                authState = (AuthState) localContext.getAttribute(ClientContext.TARGET_AUTH_STATE);
                authhost = (HttpHost) localContext.getAttribute(ExecutionContext.HTTP_TARGET_HOST);
            }
            if (sc == HttpStatus.SC_PROXY_AUTHENTICATION_REQUIRED) {
                // Proxy authentication required
                authState = (AuthState) localContext.getAttribute(ClientContext.PROXY_AUTH_STATE);
                authhost = (HttpHost) localContext.getAttribute(ExecutionContext.HTTP_PROXY_HOST);
            }

            if (authState != null) {
                System.out.println("----------------------------------------");
                AuthScheme authscheme = authState.getAuthScheme();
                System.out.println("Please provide credentials for " + authscheme.getRealm() + "@"
                        + authhost.toHostString());

                BufferedReader console = new BufferedReader(new InputStreamReader(System.in));

                System.out.print("Enter username: ");
                String user = console.readLine();
                System.out.print("Enter password: ");
                String password = console.readLine();

                if (user != null && user.length() > 0) {
                    Credentials creds = new UsernamePasswordCredentials(user, password);
                    httpclient.getCredentialsProvider().setCredentials(new AuthScope(authhost), creds);
                    trying = true;
                } else {
                    trying = false;
                }
            } else {
                trying = false;
            }
        }

    } finally {
        // When HttpClient instance is no longer needed,
        // shut down the connection manager to ensure
        // immediate deallocation of all system resources
        httpclient.getConnectionManager().shutdown();
    }
}

From source file: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 av  a2s  . 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>() {
                @Override
                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.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   ww w.ja  v  a 2 s  .  c  o m*/
            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;//from   w  w  w  .j  a  va  2 s  .co  m
    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:com.aestel.chemistry.openEye.fp.apps.SDFFPNNFinder.java

public static void main(String... args) throws IOException {
    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;//from  w w  w. jav a 2s. 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//from   w  ww  .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);
        }
    }
}