Example usage for java.lang Exception Exception

List of usage examples for java.lang Exception Exception

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Introduction

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

Prototype

public Exception(Throwable cause)

Source Link

Document

Constructs a new exception with the specified cause and a detail message of (cause==null ?

Usage

From source file:at.co.malli.relpm.RelPM.java

/**
 * @param args the command line arguments
 *///from ww  w .j av  a  2 s.  c o m
public static void main(String[] args) {
    //<editor-fold defaultstate="collapsed" desc=" Create config & log directory ">
    String userHome = System.getProperty("user.home");
    File relPm = new File(userHome + "/.RelPM");
    if (!relPm.exists()) {
        boolean worked = relPm.mkdir();
        if (!worked) {
            ExceptionDisplayer.showErrorMessage(new Exception("Could not create directory "
                    + relPm.getAbsolutePath() + " to store user-settings and logs"));
            System.exit(-1);
        }
    }
    File userConfig = new File(relPm.getAbsolutePath() + "/RelPM-userconfig.xml"); //should be created...
    if (!userConfig.exists()) {
        try {
            URL resource = RelPM.class.getResource("/at/co/malli/relpm/RelPM-defaults.xml");
            FileUtils.copyURLToFile(resource, userConfig);
        } catch (IOException ex) {
            ExceptionDisplayer.showErrorMessage(new Exception("Could not copy default config. Reason:\n"
                    + ex.getClass().getName() + ": " + ex.getMessage()));
            System.exit(-1);
        }
    }
    if (!userConfig.canWrite() || !userConfig.canRead()) {
        ExceptionDisplayer.showErrorMessage(new Exception(
                "Can not read or write " + userConfig.getAbsolutePath() + "to store user-settings"));
        System.exit(-1);
    }
    if (System.getProperty("os.name").toLowerCase().contains("win")) {
        Path relPmPath = Paths.get(relPm.toURI());
        try {
            Files.setAttribute(relPmPath, "dos:hidden", true);
        } catch (IOException ex) {
            ExceptionDisplayer.showErrorMessage(new Exception("Could not set " + relPm.getAbsolutePath()
                    + " hidden. " + "Reason:\n" + ex.getClass().getName() + ": " + ex.getMessage()));
            System.exit(-1);
        }
    }
    //</editor-fold>

    logger.trace("Environment setup sucessfull");

    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code ">
    try {
        String wantedLookAndFeel = SettingsProvider.getInstance().getString("gui.lookAndFeel");
        UIManager.LookAndFeelInfo[] installed = UIManager.getInstalledLookAndFeels();
        boolean found = false;
        for (UIManager.LookAndFeelInfo info : installed) {
            if (info.getClassName().equals(wantedLookAndFeel))
                found = true;
        }
        if (found)
            UIManager.setLookAndFeel(wantedLookAndFeel);
        else
            UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
    } catch (ClassNotFoundException ex) {
        logger.error(ex.getMessage());
        ExceptionDisplayer.showErrorMessage(ex);
    } catch (InstantiationException ex) {
        logger.error(ex.getMessage());
        ExceptionDisplayer.showErrorMessage(ex);
    } catch (IllegalAccessException ex) {
        logger.error(ex.getMessage());
        ExceptionDisplayer.showErrorMessage(ex);
    } catch (javax.swing.UnsupportedLookAndFeelException ex) {
        logger.error(ex.getMessage());
        ExceptionDisplayer.showErrorMessage(ex);
    }
    //</editor-fold>

    //<editor-fold defaultstate="collapsed" desc=" Add GUI start to awt EventQue ">
    java.awt.EventQueue.invokeLater(new Runnable() {
        public void run() {
            new MainGUI().setVisible(true);
        }
    });
    //</editor-fold>
}

From source file:org.soasecurity.wso2.mutual.auth.oauth2.client.MutualSSLOAuthClient.java

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

    File file = new File((new File(".")).getCanonicalPath() + File.separator + "src" + File.separator + "main"
            + File.separator + "resources" + File.separator + "keystore" + File.separator + keyStoreName);

    if (!file.exists()) {
        throw new Exception("Key Store file can not be found in " + file.getCanonicalPath());
    }// w ww .  j  a  va2 s. co m

    //Set trust store, you need to import server's certificate of CA certificate chain in to this
    //key store
    System.setProperty("javax.net.ssl.trustStore", file.getCanonicalPath());
    System.setProperty("javax.net.ssl.trustStorePassword", keyStorePassword);

    //Set key store, this must contain the user private key
    //here we have use both trust store and key store as the same key store
    //But you can use a separate key store for key store an trust store.
    System.setProperty("javax.net.ssl.keyStore", file.getCanonicalPath());
    System.setProperty("javax.net.ssl.keyStorePassword", keyStorePassword);

    HttpClient client = new HttpClient();

    HttpMethod method = new PostMethod(endPoint);

    // Base64 encoded client id & secret
    method.setRequestHeader("Authorization",
            "Basic T09pN2dpUjUwdDZtUmU1ZkpmWUhVelhVa1QwYTpOOUI2dDZxQ0E2RFp2eTJPQkFIWDhjVlI1eUlh");
    method.setRequestHeader("Content-Type", "application/x-www-form-urlencoded");

    NameValuePair pair1 = new NameValuePair();
    pair1.setName("grant_type");
    pair1.setValue("x509");

    NameValuePair pair2 = new NameValuePair();
    pair2.setName("username");
    pair2.setValue("asela");

    NameValuePair pair3 = new NameValuePair();
    pair3.setName("password");
    pair3.setValue("asela");

    method.setQueryString(new NameValuePair[] { pair1, pair2, pair3 });

    int statusCode = client.executeMethod(method);

    if (statusCode != HttpStatus.SC_OK) {

        System.out.println("Failed: " + method.getStatusLine());

    } else {

        byte[] responseBody = method.getResponseBody();

        System.out.println(new String(responseBody));
    }
}

From source file:com.congiu.load.csv.Main.java

public static void main(String[] args) {
    Options opts = buildCommandLineOptions();

    Configuration conf = new Configuration();

    try {//from   w  w w. j a  v  a2 s .  c o  m
        CommandLine cmd = processArguments(opts, args);

        if (cmd.hasOption(OPT_HELP[0])) {
            printUsage(opts, new PrintWriter(System.out));
            System.exit(0);
        }

        // all unprocessed arguments are files.
        // let's first check if they all exist
        for (String s : cmd.getArgs()) {
            if (!FSUtils.fileExists(conf, s)) {
                throw new Exception("File " + s + " does not exist.");
            }
        }

        CSVConverter converter = getCSVConverter(cmd);

        for (String s : cmd.getArgs()) {

        }

    } catch (Exception ex) {
        System.err.println("There was a problem parsing your arguments.");
        System.err.println(ex);
        printUsage(opts, new PrintWriter(System.err));
        System.exit(-1);
    }
}

From source file:com.floragunn.searchguard.tools.Hasher.java

public static void main(final String[] args) {

    final Options options = new Options();
    final HelpFormatter formatter = new HelpFormatter();
    options.addOption(//from w  w  w.  j  a v  a2  s.co  m
            Option.builder("p").argName("password").hasArg().desc("Cleartext password to hash").build());
    options.addOption(Option.builder("env").argName("name environment variable").hasArg()
            .desc("name environment variable to read password from").build());

    final CommandLineParser parser = new DefaultParser();
    try {
        final CommandLine line = parser.parse(options, args);

        if (line.hasOption("p")) {
            System.out.println(hash(line.getOptionValue("p").getBytes("UTF-8")));
        } else if (line.hasOption("env")) {
            final String pwd = System.getenv(line.getOptionValue("env"));
            if (pwd == null || pwd.isEmpty()) {
                throw new Exception("No environment variable '" + line.getOptionValue("env") + "' set");
            }
            System.out.println(hash(pwd.getBytes("UTF-8")));
        } else {
            final Console console = System.console();
            if (console == null) {
                throw new Exception("Cannot allocate a console");
            }
            final char[] passwd = console.readPassword("[%s]", "Password:");
            System.out.println(hash(new String(passwd).getBytes("UTF-8")));
        }
    } catch (final Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        formatter.printHelp("hasher.sh", options, true);
        System.exit(-1);
    }
}

From source file:gov.nih.nci.ncicb.tcga.dcc.qclive.loader.CommandLineLoader.java

public static void main(final String[] args) {
    try {//from   w w w  .  j  a  va2 s  . co  m
        if (args.length != 1) {
            throw new Exception("Expected filename argument");
        }
        configureDataSource();
        configureDccCommonDataSource();
        List<FileListRecord> fileList = readFileList(args[0]);
        CommandLineLoader cll = new CommandLineLoader(fileList);
        cll.go();
    } catch (Exception e) { //catch everything including runtime exceptions
        logger.logToLogger(Level.ERROR, String.format("ERROR: %s", e.getMessage()));
    }
}

From source file:edu.toronto.cs.xcurator.cli.CLIRunner.java

public static void main(String[] args) {
    Options options = setupOptions();/*from  ww  w  .  j a v a2 s .co  m*/
    CommandLineParser parser = new BasicParser();
    try {
        CommandLine line = parser.parse(options, args);
        if (line.hasOption('t')) {
            fileType = line.getOptionValue('t');
        } else {
            fileType = XML;
        }
        if (line.hasOption('o')) {
            tdbDirectory = line.getOptionValue('o');
            File d = new File(tdbDirectory);
            if (!d.exists() || !d.isDirectory()) {
                throw new Exception("TDB directory does not exist, please create.");
            }
        }
        if (line.hasOption('h')) {
            domain = line.getOptionValue('h');
            try {
                URL url = new URL(domain);
            } catch (MalformedURLException ex) {
                throw new Exception("The domain name is ill-formed");
            }
        } else {
            printHelpAndExit(options);
        }
        if (line.hasOption('m')) {
            serializeMapping = true;
            mappingFilename = line.getOptionValue('m');
        }
        if (line.hasOption('d')) {
            dirLocation = line.getOptionValue('d');
            inputStreams = new ArrayList<>();
            final List<String> files = Util.getFiles(dirLocation);
            for (String inputfile : files) {
                File f = new File(inputfile);
                if (f.isFile() && f.exists()) {
                    System.out.println("Adding document to mapping discoverer: " + inputfile);
                    inputStreams.add(new FileInputStream(f));
                } // If it is a URL download link for the document from SEC
                else if (inputfile.startsWith("http") && inputfile.contains("://")) {
                    // Download
                    System.out.println("Adding remote document to mapping discoverer: " + inputfile);
                    try {
                        URL url = new URL(inputfile);
                        InputStream remoteDocumentStream = url.openStream();
                        inputStreams.add(remoteDocumentStream);
                    } catch (MalformedURLException ex) {
                        throw new Exception("The document URL is ill-formed: " + inputfile);
                    } catch (IOException ex) {
                        throw new Exception("Error in downloading remote document: " + inputfile);
                    }
                } else {
                    throw new Exception("Cannot open XBRL document: " + f.getName());
                }
            }
        }

        if (line.hasOption('f')) {
            fileLocation = line.getOptionValue('f');
            inputStreams = new ArrayList<>();
            File f = new File(fileLocation);
            if (f.isFile() && f.exists()) {
                System.out.println("Adding document to mapping discoverer: " + fileLocation);
                inputStreams.add(new FileInputStream(f));
            } // If it is a URL download link for the document from SEC
            else if (fileLocation.startsWith("http") && fileLocation.contains("://")) {
                // Download
                System.out.println("Adding remote document to mapping discoverer: " + fileLocation);
                try {
                    URL url = new URL(fileLocation);
                    InputStream remoteDocumentStream = url.openStream();
                    inputStreams.add(remoteDocumentStream);
                } catch (MalformedURLException ex) {
                    throw new Exception("The document URL is ill-formed: " + fileLocation);
                } catch (IOException ex) {
                    throw new Exception("Error in downloading remote document: " + fileLocation);
                }
            } else {

                throw new Exception("Cannot open XBRL document: " + f.getName());
            }

        }

        setupDocumentBuilder();
        RdfFactory rdfFactory = new RdfFactory(new RunConfig(domain));
        List<Document> documents = new ArrayList<>();
        for (InputStream inputStream : inputStreams) {
            Document dataDocument = null;
            if (fileType.equals(JSON)) {
                String json = IOUtils.toString(inputStream);
                final String xml = Util.json2xml(json);
                final InputStream xmlInputStream = IOUtils.toInputStream(xml);
                dataDocument = createDocument(xmlInputStream);
            } else {
                dataDocument = createDocument(inputStream);
            }
            documents.add(dataDocument);
        }
        if (serializeMapping) {
            System.out.println("Mapping file will be saved to: " + new File(mappingFilename).getAbsolutePath());
            rdfFactory.createRdfs(documents, tdbDirectory, mappingFilename);
        } else {
            rdfFactory.createRdfs(documents, tdbDirectory);
        }
    } catch (Exception ex) {
        ex.printStackTrace();
        System.err.println("Unexpected exception: " + ex.getMessage());
        System.exit(1);
    }
}

From source file:mase.stat.MasterTournament.java

public static void main(String[] args) throws Exception {
    List<File> sampleFolders = new ArrayList<>();
    List<File> testFolders = new ArrayList<>();
    int freq = 0;
    String name = "";
    boolean self = false;
    String individuals = null;/*from w  w  w.j av  a2  s .c o  m*/
    int elite = 0;

    for (int x = 0; x < args.length; x++) {
        if (args[x].equalsIgnoreCase(TEST_FOLDER)) {
            File folder = new File(args[1 + x++]);
            if (!folder.exists()) {
                throw new Exception("Folder does not exist: " + folder.getAbsolutePath());
            }
            testFolders.add(folder);
        } else if (args[x].equalsIgnoreCase(SAMPLE_FOLDER)) {
            File folder = new File(args[1 + x++]);
            if (!folder.exists()) {
                throw new Exception("Folder does not exist: " + folder.getAbsolutePath());
            }
            sampleFolders.add(folder);
        } else if (args[x].equalsIgnoreCase(BOTH_FOLDER)) {
            File folder = new File(args[1 + x++]);
            if (!folder.exists()) {
                throw new Exception("Folder does not exist: " + folder.getAbsolutePath());
            }
            sampleFolders.add(folder);
            testFolders.add(folder);
        } else if (args[x].equalsIgnoreCase(FREQUENCY)) {
            freq = Integer.parseInt(args[1 + x++]);
        } else if (args[x].equalsIgnoreCase(ELITE)) {
            elite = Integer.parseInt(args[1 + x++]);
        } else if (args[x].equalsIgnoreCase(OUTNAME)) {
            name = args[1 + x++];
        } else if (args[x].equalsIgnoreCase(SELF)) {
            self = true;
        } else if (args[x].equalsIgnoreCase(INDIVIDUALS)) {
            individuals = args[1 + x++];
        }
    }

    if (testFolders.isEmpty() || sampleFolders.isEmpty()) {
        System.out.println("Nothing to evaluate!");
        return;
    }

    MaseProblem sim = Reevaluate.createSimulator(args);
    MasterTournament mt = new MasterTournament(sampleFolders, testFolders, sim, name);

    if (individuals != null) {
        mt.makeIndsTournaments(individuals);
    } else if (self) {
        mt.makeSelfTournaments(freq);
    } else {
        mt.makeSampleTournaments(freq, elite);
    }

    mt.executor.shutdown();
}

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

public static void main(String[] args) throws Exception {
    final KmerStartsWriter out;
    final boolean translQuery;
    final int wordSize;
    final int translTable;

    try {/*from   w  w w.j  a v  a2  s .c  o  m*/
        CommandLine cmdLine = new PosixParser().parse(options, args);
        args = cmdLine.getArgs();

        if (args.length < 2) {
            throw new Exception("Unexpected number of arguments");
        }

        if (cmdLine.hasOption("out")) {
            out = new KmerStartsWriter(cmdLine.getOptionValue("out"));
        } else {
            out = new KmerStartsWriter(System.out);
        }

        if (cmdLine.hasOption("transl-table")) {
            translTable = Integer.valueOf(cmdLine.getOptionValue("transl-table"));
        } else {
            translTable = 11;
        }

        translQuery = cmdLine.hasOption("transl-kmer");
        wordSize = Integer.valueOf(args[0]);

    } catch (Exception e) {
        new HelpFormatter().printHelp("KmerStartsFromKnown <word_size> [name=]<ref_file> ...", options);
        System.err.println(e.getMessage());
        System.exit(1);
        throw new RuntimeException("Stupid jvm"); //While this will never get thrown it is required to make sure javac doesn't get confused about uninitialized variables
    }

    long startTime = System.currentTimeMillis();

    /*
     * if (args.length == 4) { maxThreads = Integer.valueOf(args[3]); } else
     * {
     */

    //}

    System.err.println("Starting kmer mapping at " + new Date());
    System.err.println("*  References:              " + Arrays.asList(args));
    System.err.println("*  Kmer length:             " + wordSize);

    for (int index = 1; index < args.length; index++) {
        String refName;
        String refFileName = args[index];
        if (refFileName.contains("=")) {
            String[] lexemes = refFileName.split("=");
            refName = lexemes[0];
            refFileName = lexemes[1];
        } else {
            String tmpName = new File(refFileName).getName();
            if (tmpName.contains(".")) {
                refName = tmpName.substring(0, tmpName.lastIndexOf("."));
            } else {
                refName = tmpName;
            }
        }

        File refFile = new File(refFileName);

        if (SeqUtils.guessSequenceType(refFile) != SequenceType.Nucleotide) {
            throw new Exception("Reference file " + refFile + " contains " + SeqUtils.guessFileFormat(refFile)
                    + " sequences but expected nucleotide sequences");
        }

        SequenceReader seqReader = new SequenceReader(refFile);
        Sequence seq;

        while ((seq = seqReader.readNextSequence()) != null) {
            if (seq.getSeqName().startsWith("#")) {
                continue;
            }
            ModelPositionKmerGenerator kmers = new ModelPositionKmerGenerator(seq.getSeqString(), wordSize,
                    SequenceType.Nucleotide);

            for (char[] charmer : kmers) {
                int pos = kmers.getModelPosition() - 1;
                if (translQuery) {
                    if (pos % 3 != 0) {
                        continue;
                    } else {
                        pos /= 3;
                    }
                }

                String kmer = new String(charmer);

                out.write(new KmerStart(refName, seq.getSeqName(), seq.getSeqName(), kmer, 1, pos, translQuery,
                        (translQuery ? ProteinUtils.getInstance().translateToProtein(kmer, true, translTable)
                                : null)));

            }
        }
        seqReader.close();
    }
    out.close();
}

From source file:com.thinkbiganalytics.kerberos.TestKerberosKinit.java

public static void main(String[] args) throws Exception {
    final TestKerberosKinit testKerberosKinit = new TestKerberosKinit();
    Scanner scanner = new Scanner(System.in);

    System.out.println(" ");
    System.out.print("Which environment are you in? Enter 1 for HDP or 2 for Cloudera: ");
    String environmentCode = scanner.nextLine();
    if (StringUtils.isEmpty(environmentCode)) {
        environmentCode = "1";
    }/*from  w  w w  .ja v  a2s .c  o m*/

    String environment;
    switch (environmentCode) {
    case "1":
        environment = ENVIRONMENT_HDP;
        break;
    case "2":
        environment = ENVIRONMENT_CLOUDERA;
        break;
    default:
        throw new Exception("Invalid environment code");
    }

    System.out.println(" ");
    System.out.println(
            "Hit enter to default to: /etc/hadoop/conf/core-site.xml,/etc/hadoop/conf/hdfs-site.xml,/usr/hdp/current/hive-client/conf/hive-site.xml");
    System.out.print("Please enter the list of configuration resources: ");
    String configResources = scanner.nextLine();
    if (StringUtils.isEmpty(configResources)) {
        configResources = "/etc/hadoop/conf/core-site.xml,/etc/hadoop/conf/hdfs-site.xml,/usr/hdp/current/hive-client/conf/hive-site.xml";
    }

    System.out.println(" ");
    System.out.println("Hit enter to default to: /etc/security/keytabs/hive-thinkbig.headless.keytab");
    System.out.print("Please enter the keytab file location: ");
    String keytab = scanner.nextLine();
    if (StringUtils.isEmpty(keytab)) {
        keytab = "/etc/security/keytabs/hive-thinkbig.headless.keytab";
    }

    System.out.println(" ");
    System.out.println("Hit enter to default to: hive/sandbox.hortonworks.com@sandbox.hortonworks.com");
    System.out.print("Please enter the real user principal name: ");
    String realUserPrincipal = scanner.nextLine();
    if (StringUtils.isEmpty(realUserPrincipal)) {
        realUserPrincipal = "hive/sandbox.hortonworks.com@sandbox.hortonworks.com";
    }

    System.out.println(" ");
    System.out.println("Please enter Y/N (default is N)");
    System.out.print("Do you want to test with a proxy user: ");
    String proxyUser = scanner.nextLine();
    if (StringUtils.isEmpty(realUserPrincipal)) {
        proxyUser = "N";
    }

    System.out.println(" ");
    System.out.println("Hit enter to default to: hdfs://sandbox.hortonworks.com:8020");
    System.out.print("Please enter the HDFS URL: ");
    String hdfsUrl = scanner.nextLine();
    if (StringUtils.isEmpty(hdfsUrl)) {
        hdfsUrl = "hdfs://sandbox.hortonworks.com:8020";
    }

    System.out.println(" ");
    System.out.println("Hit enter to default to: jdbc:hive2://localhost:10000/default");
    System.out.print("Please enter the Hive base connection string: ");
    String hiveHost = scanner.nextLine();
    if (StringUtils.isEmpty(hiveHost)) {
        hiveHost = "jdbc:hive2://localhost:10000/default";
    }

    String proxyUserName = null;
    if ("Y".equalsIgnoreCase(proxyUser)) {
        System.out.println(" ");
        System.out.print("Please enter the proxy user: ");
        proxyUserName = scanner.next();
    }

    System.out.println(" ");
    System.out.println("Executing Kinit to generate a kerberos ticket");

    if ("Y".equalsIgnoreCase(proxyUser)) {
        System.out.println("Testing with the proxy user: " + proxyUserName);
        testKerberosKinit.testHdfsWithUserImpersonation(configResources, keytab, realUserPrincipal,
                proxyUserName, environment, hdfsUrl);

        //testKerberosKinit.testHiveJdbcConnectionWithUserImpersonation(configResources, keytab, realUserPrincipal, proxyUserName);
        testKerberosKinit.testHiveJdbcConnection(configResources, keytab, realUserPrincipal, proxyUserName,
                hiveHost);
    } else {
        System.out.println("No Proxy User");
        testKerberosKinit.testHdfsAsKerberosUser(configResources, keytab, realUserPrincipal, environment,
                hdfsUrl);
        testKerberosKinit.testHiveJdbcConnection(configResources, keytab, realUserPrincipal, null, hiveHost);
    }
}

From source file:edu.msu.cme.rdp.probematch.cli.PrimerMatch.java

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

    PrintStream out = new PrintStream(System.out);
    int maxDist = Integer.MAX_VALUE;

    try {/*from ww w . ja  v a 2 s  .  c  om*/
        CommandLine line = new PosixParser().parse(options, args);
        if (line.hasOption("outFile")) {
            out = new PrintStream(new File(line.getOptionValue("outFile")));
        }
        if (line.hasOption("maxDist")) {
            maxDist = Integer.valueOf(line.getOptionValue("maxDist"));
        }
        args = line.getArgs();

        if (args.length != 2) {
            throw new Exception("Unexpected number of command line arguments");
        }
    } catch (Exception e) {
        System.err.println("Error: " + e.getMessage());
        new HelpFormatter().printHelp("PrimerMatch <primer_list | primer_file> <seq_file>", options);
        return;
    }

    List<PatternBitMask64> primers = new ArrayList();
    if (new File(args[0]).exists()) {
        File primerFile = new File(args[0]);
        SequenceFormat seqformat = SeqUtils.guessFileFormat(primerFile);

        if (seqformat.equals(SequenceFormat.FASTA)) {
            SequenceReader reader = new SequenceReader(primerFile);
            Sequence seq;

            while ((seq = reader.readNextSequence()) != null) {
                primers.add(new PatternBitMask64(seq.getSeqString(), true, seq.getSeqName()));
            }
            reader.close();
        } else {
            BufferedReader reader = new BufferedReader(new FileReader(args[0]));
            String line;

            while ((line = reader.readLine()) != null) {
                line = line.trim();
                if (!line.equals("")) {
                    primers.add(new PatternBitMask64(line, true));
                }
            }
            reader.close();
        }
    } else {
        for (String primer : args[0].split(",")) {
            primers.add(new PatternBitMask64(primer, true));
        }
    }

    SeqReader seqReader = new SequenceReader(new File(args[1]));
    Sequence seq;
    String primerRegion;

    out.println("#seqname\tdesc\tprimer_index\tprimer_name\tposition\tmismatches\tseq_primer_region");
    while ((seq = seqReader.readNextSequence()) != null) {
        for (int index = 0; index < primers.size(); index++) {
            PatternBitMask64 primer = primers.get(index);
            BitVector64Result results = BitVector64.process(seq.getSeqString().toCharArray(), primer, maxDist);

            for (BitVector64Match result : results.getResults()) {
                primerRegion = seq.getSeqString().substring(
                        Math.max(0, result.getPosition() - primer.getPatternLength()), result.getPosition());

                if (result.getPosition() < primer.getPatternLength()) {
                    for (int pad = result.getPosition(); pad < primer.getPatternLength(); pad++) {
                        primerRegion = "x" + primerRegion;
                    }
                }

                out.println(seq.getSeqName() + "\t" + seq.getDesc() + "\t" + (index + 1) + "\t"
                        + primer.getPrimerName() + "\t" + result.getPosition() + "\t" + result.getScore() + "\t"
                        + primerRegion);
            }
        }
    }
    out.close();
    seqReader.close();
}