Example usage for java.lang String equalsIgnoreCase

List of usage examples for java.lang String equalsIgnoreCase

Introduction

In this page you can find the example usage for java.lang String equalsIgnoreCase.

Prototype

public boolean equalsIgnoreCase(String anotherString) 

Source Link

Document

Compares this String to another String , ignoring case considerations.

Usage

From source file:me.ryandowling.TwitchTools.java

public static void main(String[] args) {
    loadSettings();//from  w w  w. j  av a  2s  .  c  om

    Runtime.getRuntime().addShutdownHook(new Thread() {
        @Override
        public void run() {
            saveSettings();
        }
    });

    if (args.length == 0) {
        System.err.println("Invalid number of arguments specified!");
        System.exit(1);
    } else if (args.length >= 1 && args.length <= 4) {
        switch (args[0]) {
        case "Followers":
            if (args.length == 4) {
                new Followers(args[1], Integer.parseInt(args[2]), Boolean.parseBoolean(args[3])).run();
            } else {
                System.err.println("Invalid number of arguments specified!");
                System.exit(1);
            }
            break;
        case "MicrophoneStatus":
            if (args.length == 3) {
                final int delay = Integer.parseInt(args[1]);
                final boolean guiDisplay = Boolean.parseBoolean(args[2]);

                new MicrophoneStatus(delay, guiDisplay);
            } else {
                System.err.println("Invalid number of arguments specified!");
                System.err.println("Arguments are: [delay in ms for updates] [if the gui should show]!");
                System.err.println("For example: [100] [true]!");
                System.exit(1);
            }
            break;
        case "NowPlayingConverter":
            if (args.length == 2) {
                final int delay = Integer.parseInt(args[1]);
                new NowPlayingConverter(delay).run();
            } else {
                System.err.println("Invalid number of arguments specified!");
                System.err.println("Arguments are: [delay in ms for updates]!");
                System.err.println("For example: [100]!");
                System.exit(1);
            }
            break;
        case "MusicCreditsGenerator":
            if (args.length == 2) {
                final String type = args[1];

                if (type.equalsIgnoreCase("html") || type.equalsIgnoreCase("october")
                        || type.equalsIgnoreCase("markdown")) {
                    new MusicCreditsGenerator(type).run();
                } else {
                    System.err.println("Invalid type argument specified!");
                    System.err.println("Arguments are: [type of output to generate (html|markdown|october)]!");
                    System.err.println("For example: [html]!");
                    System.exit(1);
                }
            } else {
                System.err.println("Invalid number of arguments specified!");
                System.err.println("Arguments are: [delay in ms for updates]!");
                System.err.println("For example: [100]!");
                System.exit(1);
            }
            break;
        case "SteamGamesGenerator":
            if (args.length == 2) {
                final String type = args[1];

                if (type.equalsIgnoreCase("october")) {
                    new SteamGamesGenerator(type).run();
                } else {
                    System.err.println("Invalid type argument specified!");
                    System.err.println("Arguments are: [type of output to generate (october)]!");
                    System.err.println("For example: [october]!");
                    System.exit(1);
                }
            } else {
                System.err.println("Invalid number of arguments specified!");
                System.err.println("Arguments are: [delay in ms for updates]!");
                System.err.println("For example: [100]!");
                System.exit(1);
            }
            break;
        case "FoobarControls":
            if (args.length == 1) {
                new FoobarControls().run();
            } else {
                System.err.println("Invalid number of arguments specified!");
                System.err.println("There are no arguments to provide!");
                System.exit(1);
            }
            break;
        default:
            System.err.println("Invalid tool name specified!");
            System.exit(1);
        }
    }
}

From source file:com.ibm.crail.storage.StorageServer.java

public static void main(String[] args) throws Exception {
    Logger LOG = CrailUtils.getLogger();
    CrailConfiguration conf = new CrailConfiguration();
    CrailConstants.updateConstants(conf);
    CrailConstants.printConf();/*from   w  w w . ja v  a2s.co  m*/
    CrailConstants.verify();

    int splitIndex = 0;
    for (String param : args) {
        if (param.equalsIgnoreCase("--")) {
            break;
        }
        splitIndex++;
    }

    //default values
    StringTokenizer tokenizer = new StringTokenizer(CrailConstants.STORAGE_TYPES, ",");
    if (!tokenizer.hasMoreTokens()) {
        throw new Exception("No storage types defined!");
    }
    String storageName = tokenizer.nextToken();
    int storageType = 0;
    HashMap<String, Integer> storageTypes = new HashMap<String, Integer>();
    storageTypes.put(storageName, storageType);
    for (int type = 1; tokenizer.hasMoreElements(); type++) {
        String name = tokenizer.nextToken();
        storageTypes.put(name, type);
    }
    int storageClass = -1;

    //custom values
    if (args != null) {
        Option typeOption = Option.builder("t").desc("storage type to start").hasArg().build();
        Option classOption = Option.builder("c").desc("storage class the server will attach to").hasArg()
                .build();
        Options options = new Options();
        options.addOption(typeOption);
        options.addOption(classOption);
        CommandLineParser parser = new DefaultParser();

        try {
            CommandLine line = parser.parse(options, Arrays.copyOfRange(args, 0, splitIndex));
            if (line.hasOption(typeOption.getOpt())) {
                storageName = line.getOptionValue(typeOption.getOpt());
                storageType = storageTypes.get(storageName).intValue();
            }
            if (line.hasOption(classOption.getOpt())) {
                storageClass = Integer.parseInt(line.getOptionValue(classOption.getOpt()));
            }
        } catch (ParseException e) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("Storage tier", options);
            System.exit(-1);
        }
    }
    if (storageClass < 0) {
        storageClass = storageType;
    }

    StorageTier storageTier = StorageTier.createInstance(storageName);
    if (storageTier == null) {
        throw new Exception("Cannot instantiate datanode of type " + storageName);
    }

    String extraParams[] = null;
    splitIndex++;
    if (args.length > splitIndex) {
        extraParams = new String[args.length - splitIndex];
        for (int i = splitIndex; i < args.length; i++) {
            extraParams[i - splitIndex] = args[i];
        }
    }
    storageTier.init(conf, extraParams);
    storageTier.printConf(LOG);

    RpcClient rpcClient = RpcClient.createInstance(CrailConstants.NAMENODE_RPC_TYPE);
    rpcClient.init(conf, args);
    rpcClient.printConf(LOG);

    ConcurrentLinkedQueue<InetSocketAddress> namenodeList = CrailUtils.getNameNodeList();
    ConcurrentLinkedQueue<RpcConnection> connectionList = new ConcurrentLinkedQueue<RpcConnection>();
    while (!namenodeList.isEmpty()) {
        InetSocketAddress address = namenodeList.poll();
        RpcConnection connection = rpcClient.connect(address);
        connectionList.add(connection);
    }
    RpcConnection rpcConnection = connectionList.peek();
    if (connectionList.size() > 1) {
        rpcConnection = new RpcDispatcher(connectionList);
    }
    LOG.info("connected to namenode(s) " + rpcConnection.toString());

    StorageServer server = storageTier.launchServer();
    StorageRpcClient storageRpc = new StorageRpcClient(storageType, CrailStorageClass.get(storageClass),
            server.getAddress(), rpcConnection);

    HashMap<Long, Long> blockCount = new HashMap<Long, Long>();
    long sumCount = 0;
    while (server.isAlive()) {
        StorageResource resource = server.allocateResource();
        if (resource == null) {
            break;
        } else {
            storageRpc.setBlock(resource.getAddress(), resource.getLength(), resource.getKey());
            DataNodeStatistics stats = storageRpc.getDataNode();
            long newCount = stats.getFreeBlockCount();
            long serviceId = stats.getServiceId();

            long oldCount = 0;
            if (blockCount.containsKey(serviceId)) {
                oldCount = blockCount.get(serviceId);
            }
            long diffCount = newCount - oldCount;
            blockCount.put(serviceId, newCount);
            sumCount += diffCount;
            LOG.info("datanode statistics, freeBlocks " + sumCount);
        }
    }

    while (server.isAlive()) {
        DataNodeStatistics stats = storageRpc.getDataNode();
        long newCount = stats.getFreeBlockCount();
        long serviceId = stats.getServiceId();

        long oldCount = 0;
        if (blockCount.containsKey(serviceId)) {
            oldCount = blockCount.get(serviceId);
        }
        long diffCount = newCount - oldCount;
        blockCount.put(serviceId, newCount);
        sumCount += diffCount;

        LOG.info("datanode statistics, freeBlocks " + sumCount);
        Thread.sleep(2000);
    }
}

From source file:edu.msu.cme.rdp.classifier.ClassifierCmd.java

/**
 * This is the main method to do classification.
 * <p>Usage: java ClassifierCmd queryFile outputFile [property file].
 * <br>//from   w  ww.  ja  v a2  s  . c om
 * queryFile can be one of the following formats: Fasta, Genbank and EMBL. 
 * <br>
 * outputFile will be used to save the classification output.
 * <br>
 * property file contains the mapping of the training files.
 * <br>
 * Note: the training files and the property file should be in the same directory.
 * The default property file is set to data/classifier/16srrna/rRNAClassifier.properties.
 */
public static void main(String[] args) throws Exception {

    String queryFile = null;
    String outputFile = null;
    String propFile = null;
    String gene = null;
    ClassificationResultFormatter.FORMAT format = CmdOptions.DEFAULT_FORMAT;
    int min_bootstrap_words = Classifier.MIN_BOOTSTRSP_WORDS;

    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption(CmdOptions.OUTFILE_SHORT_OPT)) {
            outputFile = line.getOptionValue(CmdOptions.OUTFILE_SHORT_OPT);
        } else {
            throw new Exception("outputFile must be specified");
        }

        if (line.hasOption(CmdOptions.TRAINPROPFILE_SHORT_OPT)) {
            if (gene != null) {
                throw new IllegalArgumentException(
                        "Already specified the gene from the default location. Can not specify train_propfile");
            } else {
                propFile = line.getOptionValue(CmdOptions.TRAINPROPFILE_SHORT_OPT);
            }
        }
        if (line.hasOption(CmdOptions.FORMAT_SHORT_OPT)) {
            String f = line.getOptionValue(CmdOptions.FORMAT_SHORT_OPT);
            if (f.equalsIgnoreCase("allrank")) {
                format = ClassificationResultFormatter.FORMAT.allRank;
            } else if (f.equalsIgnoreCase("fixrank")) {
                format = ClassificationResultFormatter.FORMAT.fixRank;
            } else if (f.equalsIgnoreCase("filterbyconf")) {
                format = ClassificationResultFormatter.FORMAT.filterbyconf;
            } else if (f.equalsIgnoreCase("db")) {
                format = ClassificationResultFormatter.FORMAT.dbformat;
            } else {
                throw new IllegalArgumentException(
                        "Not valid output format, only allrank, fixrank, filterbyconf and db allowed");
            }
        }
        if (line.hasOption(CmdOptions.GENE_SHORT_OPT)) {
            if (propFile != null) {
                throw new IllegalArgumentException(
                        "Already specified train_propfile. Can not specify gene any more");
            }
            gene = line.getOptionValue(CmdOptions.GENE_SHORT_OPT).toLowerCase();

            if (!gene.equals(ClassifierFactory.RRNA_16S_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)) {
                throw new IllegalArgumentException(gene + " is NOT valid, only allows "
                        + ClassifierFactory.RRNA_16S_GENE + " and " + ClassifierFactory.FUNGALLSU_GENE);
            }
        }
        if (line.hasOption(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT)) {
            min_bootstrap_words = Integer
                    .parseInt(line.getOptionValue(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT));
            if (min_bootstrap_words < Classifier.MIN_BOOTSTRSP_WORDS) {
                throw new IllegalArgumentException(CmdOptions.MIN_BOOTSTRAP_WORDS_LONG_OPT
                        + " must be at least " + Classifier.MIN_BOOTSTRSP_WORDS);
            }
        }

        args = line.getArgs();
        if (args.length != 1) {
            throw new Exception("Expect one query file");
        }
        queryFile = args[0];

    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(120,
                "ClassifierCmd [options] <samplefile>\nNote this is the legacy command for one sample classification ",
                "", options, "");

        return;
    }

    if (propFile == null && gene == null) {
        gene = CmdOptions.DEFAULT_GENE;
    }
    ClassifierCmd classifierCmd = new ClassifierCmd();

    printLicense();
    classifierCmd.doClassify(queryFile, outputFile, propFile, format, gene, min_bootstrap_words);

}

From source file:com.datastax.dse.demos.solr.Wikipedia.java

public static void main(String[] args) {

    if (args.length == 0)
        usage();/*from  w w w.j av a2s .  c  om*/

    System.out.println("args: " + Arrays.asList(args));

    // parse args
    for (int i = 0; i < args.length; i = i + 2) {

        if (args[i].startsWith("--")) {
            try {
                String arg = args[i].substring(2);
                String value = args[i + 1];

                if (arg.equalsIgnoreCase("wikifile"))
                    wikifile = value;
                if (arg.equalsIgnoreCase("limit"))
                    limit = Integer.parseInt(value);
                if (arg.equalsIgnoreCase("host"))
                    host = value;
                if (arg.equalsIgnoreCase("scheme"))
                    scheme = value;
                if (arg.equalsIgnoreCase("user"))
                    user = value;
                if (arg.equalsIgnoreCase("password"))
                    password = value;
            } catch (Throwable t) {
                usage();
            }
        }
    }
    url = String.format(urlTemplate, scheme, host);
    // Initialize Solr with our custom HTTP Client helpers - which handle
    // SSL & Kerberos. We must have dse.yaml on the classpath for this
    try {
        if (DseConfig.isSslEnabled()) {
            SolrHttpClientInitializer
                    .initEncryption(new EncryptionOptions().withSSLContext(DseConfig.getSSLContext())
                            .withHostnameVerifier(SSLSocketFactory.ALLOW_ALL_HOSTNAME_VERIFIER));
        }

        if (DseConfig.isKerberosEnabled()) {
            // Obtain kerberos credentials from local ticket cache
            AuthenticationOptions options = new AuthenticationOptions();
            if (DseConfig.isSslEnabled()) {
                options.withSSLContext(DseConfig.getSSLContext())
                        .withHostnameVerifier(SSLSocketFactory.ALLOW_ALL_HOSTNAME_VERIFIER);
            }

            SolrHttpClientInitializer.initAuthentication(options);
        }
    } catch (Exception e) {
        System.out.println("Fatal error when initializing Solr clients, exiting");
        e.printStackTrace();
        System.exit(1);
    }

    System.out.println("Start indexing wikipedia...");
    long startTime = System.currentTimeMillis();

    indexWikipedia();

    long endTime = System.currentTimeMillis();

    System.out.println("Finished");

    System.exit(0);

}

From source file:io.github.the28awg.okato.App.java

public static void main(String[] args) {
    Options options = new Options();

    options.addOption(Option.builder().longOpt("token").hasArg().required().argName("token")
            .desc(" ? ?  ??").build());
    options.addOption(Option.builder("t").longOpt("type").hasArg().required().argName("type")
            .desc("  [city, street, building]").build());
    options.addOption(Option.builder("q").longOpt("query").hasArg().argName("query")
            .desc(" ? ?  ").build());
    options.addOption(Option.builder("c").longOpt("city_id").hasArg().argName("city_id")
            .desc("  (? )").build());
    options.addOption(Option.builder("s").longOpt("street_id").hasArg().argName("street_id")
            .desc(" ").build());

    CommandLineParser parser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd;// w  w w .  jav a2  s .  c  o m

    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        formatter.printHelp("okato", options);
        System.exit(1);
        return;
    }

    AddressFactory.token(cmd.getOptionValue("token"));

    String arg_type = cmd.getOptionValue("type");
    String arg_city_id = cmd.getOptionValue("city_id", "");
    String arg_street_id = cmd.getOptionValue("street_id", "");
    String arg_query = cmd.getOptionValue("query", "");
    if (arg_type.equalsIgnoreCase("city")) {
        try {
            log(SimpleOkato.toSimpleResponse(
                    AddressFactory.service().city(AddressFactory.token(), arg_query).execute().body()));
        } catch (IOException e) {
            e.printStackTrace();
        }
    } else if (arg_type.equalsIgnoreCase("street")) {
        try {
            log(SimpleOkato.toSimpleResponse(AddressFactory.service()
                    .street(AddressFactory.token(), arg_city_id, arg_query).execute().body()));
        } catch (IOException e) {
            e.printStackTrace();
        }
    } else if (arg_type.equalsIgnoreCase("building")) {
        try {
            log(SimpleOkato.toSimpleResponse(AddressFactory.service()
                    .building(AddressFactory.token(), arg_city_id, arg_street_id, arg_query).execute().body()));
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

}

From source file:com.denimgroup.threadfix.importer.cli.CommandLineMigration.java

public static void main(String[] args) {

    if (!check(args))
        return;//from  www  .  j  a  va  2 s. c o m

    try {
        String inputScript = args[0];
        String inputMySqlConfig = args[1];
        String outputScript = "import.sql";
        String outputMySqlConfigTemp = "jdbc_temp.properties";
        String errorLogFile = "error.log";
        String fixedSqlFile = "error_sql.sql";
        String errorLogAttemp1 = "error1.log";
        String infoLogFile = "info.log";
        String rollbackScript = "rollback.sql";

        deleteFile(outputScript);
        deleteFile(errorLogFile);
        deleteFile(errorLogFile);
        deleteFile(fixedSqlFile);
        deleteFile(errorLogAttemp1);
        deleteFile(infoLogFile);
        deleteFile(rollbackScript);

        PrintStream infoPrintStream = new PrintStream(new FileOutputStream(new File(infoLogFile)));
        System.setOut(infoPrintStream);

        long startTime = System.currentTimeMillis();

        copyFile(inputMySqlConfig, outputMySqlConfigTemp);

        LOGGER.info("Creating threadfix table in mySql database ...");
        ScriptRunner scriptRunner = SpringConfiguration.getContext().getBean(ScriptRunner.class);

        startTime = printTimeConsumed(startTime);
        convert(inputScript, outputScript);

        startTime = printTimeConsumed(startTime);

        PrintStream errPrintStream = new PrintStream(new FileOutputStream(new File(errorLogFile)));
        System.setErr(errPrintStream);

        LOGGER.info("Sending sql script to MySQL server ...");
        scriptRunner.run(outputScript, outputMySqlConfigTemp);

        long errorCount = scriptRunner.checkRunningAndFixStatements(errorLogFile, fixedSqlFile);
        long lastCount = errorCount + 1;
        int times = 1;
        int sameFixedSet = 0;

        // Repeat
        while (errorCount > 0) {
            //Flush error log screen to other file
            errPrintStream = new PrintStream(new FileOutputStream(new File(errorLogAttemp1)));
            System.setErr(errPrintStream);

            times += 1;

            if (errorCount == lastCount) {
                sameFixedSet++;
            } else {
                sameFixedSet = 0;
            }

            LOGGER.info("Found " + errorCount + " error statements. Sending fixed sql script to MySQL server "
                    + times + " times ...");
            scriptRunner.run(fixedSqlFile, outputMySqlConfigTemp);
            lastCount = errorCount;
            errorCount = scriptRunner.checkRunningAndFixStatements(errorLogAttemp1, fixedSqlFile);

            if (errorCount > lastCount || sameFixedSet > SAME_SET_TRY_LIMIT)
                break;
        }

        if (errorCount > 0) {
            LOGGER.error("After " + times + " of trying, still found errors in sql script. "
                    + "Please check error_sql.sql and error1.log for more details.");
            LOGGER.info("Do you want to keep data in MySQL, and then import manually error statements (y/n)? ");
            try (java.util.Scanner in = new java.util.Scanner(System.in)) {
                String answer = in.nextLine();
                if (!answer.equalsIgnoreCase("y")) {
                    rollbackData(scriptRunner, outputMySqlConfigTemp, rollbackScript);
                } else {
                    LOGGER.info(
                            "Data imported to MySQL, but still have some errors. Please check error_sql.sql and error1.log to import manually.");
                }

            }

        } else {
            printTimeConsumed(startTime);
            LOGGER.info("Migration successfully finished");
        }

        deleteFile(outputMySqlConfigTemp);

    } catch (Exception e) {
        LOGGER.error("Error: ", e);
    }
}

From source file:edu.msu.cme.rdp.multicompare.Reprocess.java

/**
 * This class reprocesses the classification results (allrank output) and print out hierarchy output file, based on the confidence cutoff;
 * and print out only the detail classification results with assignment at certain rank with confidence above the cutoff or/and matching a given taxon.
 * @param args/*ww  w  . j ava 2 s  . c  om*/
 * @throws Exception 
 */
public static void main(String[] args) throws Exception {

    PrintWriter assign_out = new PrintWriter(new NullWriter());
    float conf = 0.8f;
    PrintStream heir_out = null;
    String hier_out_filename = null;
    ClassificationResultFormatter.FORMAT format = ClassificationResultFormatter.FORMAT.allRank;
    String rank = null;
    String taxonFilterFile = null;
    String train_propfile = null;
    String gene = null;
    List<MCSample> samples = new ArrayList();

    try {
        CommandLine line = new PosixParser().parse(options, args);
        if (line.hasOption(CmdOptions.HIER_OUTFILE_SHORT_OPT)) {
            hier_out_filename = line.getOptionValue(CmdOptions.HIER_OUTFILE_SHORT_OPT);
            heir_out = new PrintStream(hier_out_filename);
        } else {
            throw new Exception(
                    "It make sense to provide output filename for " + CmdOptions.HIER_OUTFILE_LONG_OPT);
        }
        if (line.hasOption(CmdOptions.OUTFILE_SHORT_OPT)) {
            assign_out = new PrintWriter(line.getOptionValue(CmdOptions.OUTFILE_SHORT_OPT));
        }

        if (line.hasOption(CmdOptions.RANK_SHORT_OPT)) {
            rank = line.getOptionValue(CmdOptions.RANK_SHORT_OPT);
        }
        if (line.hasOption(CmdOptions.TAXON_SHORT_OPT)) {
            taxonFilterFile = line.getOptionValue(CmdOptions.TAXON_SHORT_OPT);
        }

        if (line.hasOption(CmdOptions.BOOTSTRAP_SHORT_OPT)) {
            conf = Float.parseFloat(line.getOptionValue(CmdOptions.BOOTSTRAP_SHORT_OPT));
            if (conf < 0 || conf > 1) {
                throw new IllegalArgumentException("Confidence must be in the range [0,1]");
            }
        }
        if (line.hasOption(CmdOptions.FORMAT_SHORT_OPT)) {
            String f = line.getOptionValue(CmdOptions.FORMAT_SHORT_OPT);
            if (f.equalsIgnoreCase("allrank")) {
                format = ClassificationResultFormatter.FORMAT.allRank;
            } else if (f.equalsIgnoreCase("fixrank")) {
                format = ClassificationResultFormatter.FORMAT.fixRank;
            } else if (f.equalsIgnoreCase("db")) {
                format = ClassificationResultFormatter.FORMAT.dbformat;
            } else if (f.equalsIgnoreCase("filterbyconf")) {
                format = ClassificationResultFormatter.FORMAT.filterbyconf;
            } else {
                throw new IllegalArgumentException(
                        "Not valid output format, only allrank, fixrank, filterbyconf and db allowed");
            }
        }
        if (line.hasOption(CmdOptions.TRAINPROPFILE_SHORT_OPT)) {
            if (gene != null) {
                throw new IllegalArgumentException(
                        "Already specified the gene from the default location. Can not specify train_propfile");
            } else {
                train_propfile = line.getOptionValue(CmdOptions.TRAINPROPFILE_SHORT_OPT);
            }
        }
        if (line.hasOption(CmdOptions.GENE_SHORT_OPT)) {
            if (train_propfile != null) {
                throw new IllegalArgumentException(
                        "Already specified train_propfile. Can not specify gene any more");
            }
            gene = line.getOptionValue(CmdOptions.GENE_SHORT_OPT).toLowerCase();

            if (!gene.equals(ClassifierFactory.RRNA_16S_GENE) && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_warcup_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_unite_GENE)) {
                throw new IllegalArgumentException(gene + " is NOT valid, only allows "
                        + ClassifierFactory.RRNA_16S_GENE + ", " + ClassifierFactory.FUNGALLSU_GENE + ", "
                        + ClassifierFactory.FUNGALITS_warcup_GENE + " and "
                        + ClassifierFactory.FUNGALITS_unite_GENE);
            }
        }
        args = line.getArgs();
        if (args.length < 1) {
            throw new Exception("Incorrect number of command line arguments");
        }

        for (String arg : args) {
            String[] inFileNames = arg.split(",");
            String inputFile = inFileNames[0];
            File idmappingFile = null;

            if (inFileNames.length == 2) {
                idmappingFile = new File(inFileNames[1]);
                if (!idmappingFile.exists()) {
                    System.err.println("Failed to find input file \"" + inFileNames[1] + "\"");
                    return;
                }
            }

            MCSample nextSample = new MCSampleResult(inputFile, idmappingFile);
            samples.add(nextSample);

        }
    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(120,
                "Reprocess [options] <Classification_allrank_result>[,idmappingfile] ...", "", options, "");
        return;
    }

    if (train_propfile == null && gene == null) {
        gene = ClassifierFactory.RRNA_16S_GENE;
    }

    HashSet<String> taxonFilter = null;
    if (taxonFilterFile != null) {
        taxonFilter = readTaxonFilterFile(taxonFilterFile);
    }

    MultiClassifier multiClassifier = new MultiClassifier(train_propfile, gene);
    DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(heir_out, samples);
    MultiClassifierResult result = multiClassifier.multiClassificationParser(samples, conf, assign_out, format,
            rank, taxonFilter);

    result.getRoot().topDownVisit(printVisitor);

    assign_out.close();
    heir_out.close();
    if (multiClassifier.hasCopyNumber()) {
        // print copy number corrected counts
        File cn_corrected_s = new File(new File(hier_out_filename).getParentFile(),
                "cncorrected_" + hier_out_filename);
        PrintStream cn_corrected_hier_out = new PrintStream(cn_corrected_s);
        printVisitor = new DefaultPrintVisitor(cn_corrected_hier_out, samples, true);
        result.getRoot().topDownVisit(printVisitor);
        cn_corrected_hier_out.close();
    }

}

From source file:com.asquareb.kaaval.MachineKey.java

/**
 * Main method to execute as a command line utility. Provides the option to
 * encrypt a string, decrypt a encrypted string or exit from the program
 *///from w  w  w  .  java2s .  c o  m
public static void main(String[] args) {
    String originalPassword = null;
    String encryptedPassword = null;
    try {
        final BufferedReader cin = new BufferedReader(new InputStreamReader(System.in));
        System.out.print("Enter E - Encrypt,D - Decrypt,X - Exit :");
        final String choice = cin.readLine();
        final Random rand = new Random();
        boolean phraseCorrect = false;
        String app = null;
        if (choice.equalsIgnoreCase("E")) {
            System.out.print("Enter the string to encrypt :");
            originalPassword = cin.readLine();
            System.out.println("Choose a phrase of min 8 chars in length ");
            System.out.println(" Also the password should include 2 Cap,");
            System.out.println(" 2 small letters,2 numeric and 2 non alpha numeric chars");
            while (!phraseCorrect) {
                System.out.print("Enter a phrase to encrypt :");
                password = cin.readLine().toCharArray();
                phraseCorrect = PasswordRules.verifyPassword(password);
            }
            System.out.print("Enter application code :");
            app = cin.readLine();
            app += (rand.nextInt(10000));
            encryptedPassword = encrypt(originalPassword, app);
            System.out.println("Encrypted password :" + encryptedPassword);
            System.out.println("Key stored in :" + app);
            System.out.println("*** Provide the encrypted string to app team");
            System.out.println("*** Store the key file in a secure durectory");
            System.out.println("*** Inform the key file name and location to app team");
        } else if (choice.equalsIgnoreCase("D")) {
            System.out.print("Enter the string to Decrypt :");
            encryptedPassword = cin.readLine();
            System.out.print("Enter the name of key file :");
            app = cin.readLine();
            final String decryptedPassword = decrypt(encryptedPassword, app);
            System.out.print("Decrypted string :" + decryptedPassword);
        }
        return;
    } catch (KaavalException e) {
        e.PrintProtectException();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:com.referencelogic.xmlormupload.main.XmlormuploadMain.java

public static void main(String args[]) {
    PropertyConfigurator.configure("log4j.properties");
    isDebugging = log.isDebugEnabled();/*from w  w  w  .ja v  a2 s .  com*/
    for (String s : args) {
        log.debug("Processing parameter: " + s);

        if (matchRegex && matchRegexStr.equals("")) {
            matchRegexStr = s;
            log.debug("Set regex string to: " + matchRegexStr);
        }

        if (s.equalsIgnoreCase("--restrict")) {
            matchRegex = true;
            log.debug("Got restrict flag, so matching regex");
        }
    }
    new XmlormuploadMain().run();
}

From source file:edu.usf.cutr.siri.SiriParserJacksonExample.java

/**
 * Takes in a path to a JSON or XML file, parses the contents into a Siri object, 
 * and prints out the contents of the Siri object.
 * /*from   ww w  .  j  a va2s .c  o m*/
 * @param args path to the JSON or XML file located on disk
 */
public static void main(String[] args) {

    if (args[0] == null) {
        System.out.println("Proper Usage is: java JacksonSiriParserExample path-to-siri-file-to-parse");
        System.exit(0);
    }

    try {

        //Siri object we're going to instantiate based on JSON or XML data
        Siri siri = null;

        //Get example JSON or XML from file
        File file = new File(args[0]);

        System.out.println("Input file = " + file.getAbsolutePath());

        /*
         * Alternately, instead of passing in a File, a String encoded in JSON or XML can be
         * passed into Jackson for parsing.  Uncomment the below line to read the 
         * JSON or XML into the String.
         */
        //String inputExample = readFile(file);   

        String extension = FilenameUtils.getExtension(args[0]);

        if (extension.equalsIgnoreCase("json")) {
            System.out.println("Parsing JSON...");
            ObjectMapper mapper = null;

            try {
                mapper = (ObjectMapper) SiriUtils.readFromCache(SiriUtils.OBJECT_MAPPER);
            } catch (Exception e) {
                System.out.println("Error reading from cache: " + e);
            }

            if (mapper == null) {
                // instantiate ObjectMapper like normal if cache read failed
                mapper = new ObjectMapper();

                //Jackson 2.0 configuration settings
                mapper.configure(DeserializationFeature.UNWRAP_ROOT_VALUE, true);
                mapper.configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
                mapper.configure(DeserializationFeature.ACCEPT_EMPTY_STRING_AS_NULL_OBJECT, true);
                mapper.configure(DeserializationFeature.USE_JAVA_ARRAY_FOR_JSON_ARRAY, true);
                mapper.configure(DeserializationFeature.READ_ENUMS_USING_TO_STRING, true);

                //Tell Jackson to expect the JSON in PascalCase, instead of camelCase
                mapper.setPropertyNamingStrategy(new PropertyNamingStrategy.PascalCaseStrategy());
            }

            //Deserialize the JSON from the file into the Siri object
            siri = mapper.readValue(file, Siri.class);

            /*
             * Alternately, you can also deserialize the JSON from a String into the Siri object.
             * Uncomment the below line to parsing the JSON from a String instead of the File.
             */
            //siri = mapper.readValue(inputExample, Siri.class);

            //Write the ObjectMapper to the cache, to speed up parsing for the next execution
            SiriUtils.forceCacheWrite(mapper);

        }

        if (extension.equalsIgnoreCase("xml")) {
            System.out.println("Parsing XML...");
            //Use Aalto StAX implementation explicitly            
            XmlFactory f = new XmlFactory(new InputFactoryImpl(), new OutputFactoryImpl());

            JacksonXmlModule module = new JacksonXmlModule();

            /**
             * Tell Jackson that Lists are using "unwrapped" style (i.e., 
             * there is no wrapper element for list). This fixes the error
             * "com.fasterxml.jackson.databind.JsonMappingException: Can not
             * >> instantiate value of type [simple type, class >>
             * uk.org.siri.siri.VehicleMonitoringDelivery] from JSON String;
             * no >> single-String constructor/factory method (through
             * reference chain: >>
             * uk.org.siri.siri.Siri["ServiceDelivery"]->
             * uk.org.siri.siri.ServiceDel >>
             * ivery["VehicleMonitoringDelivery"])"
             * 
             * NOTE - This requires Jackson v2.1
             */
            module.setDefaultUseWrapper(false);

            /**
             * Handles "xml:lang" attribute, which is used in SIRI
             * NaturalLanguage String, and looks like: <Description
             * xml:lang="EN">b/d 1:00pm until f/n. loc al and express buses
             * run w/delays & detours. POTUS visit in MANH. Allow additional
             * travel time Details at www.mta.info</Description>
             * 
             * Passing "Value" (to match expected name in XML to map,
             * considering naming strategy) will make things work. This is
             * since JAXB uses pseudo-property name of "value" for XML Text
             * segments, whereas Jackson by default uses "" (to avoid name
             * collisions).
             * 
             * NOTE - This requires Jackson v2.1
             * 
             * NOTE - This still requires a CustomPascalCaseStrategy to
             * work. Please see the CustomPascalCaseStrategy in this app
             * that is used below.
             */
            module.setXMLTextElementName("Value");

            XmlMapper xmlMapper = null;

            try {
                xmlMapper = (XmlMapper) SiriUtils.readFromCache(SiriUtils.XML_MAPPER);
            } catch (Exception e) {
                System.out.println("Error reading from cache: " + e);
            }

            if (xmlMapper == null) {
                xmlMapper = new XmlMapper(f, module);

                xmlMapper.configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
                xmlMapper.configure(DeserializationFeature.ACCEPT_EMPTY_STRING_AS_NULL_OBJECT, true);
                xmlMapper.configure(DeserializationFeature.USE_JAVA_ARRAY_FOR_JSON_ARRAY, true);
                xmlMapper.configure(DeserializationFeature.READ_ENUMS_USING_TO_STRING, true);

                /**
                 * Tell Jackson to expect the XML in PascalCase, instead of camelCase
                 * NOTE:  We need the CustomPascalStrategy here to handle XML 
                 * namespace attributes such as xml:lang.  See the comments in 
                 * CustomPascalStrategy for details.
                 */
                xmlMapper.setPropertyNamingStrategy(new CustomPascalCaseStrategy());
            }

            //Parse the SIRI XML response            
            siri = xmlMapper.readValue(file, Siri.class);

            //Write the XmlMapper to the cache, to speed up parsing for the next execution
            SiriUtils.forceCacheWrite(xmlMapper);
        }

        //If we successfully retrieved and parsed JSON or XML, print the contents
        if (siri != null) {
            SiriUtils.printContents(siri);
        }

    } catch (IOException e) {
        System.err.println("Error reading or parsing input file: " + e);
    }

}