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:Main.java

public static String checkWifiConnection(final Activity activity) throws Exception {
    ConnectivityManager connManager = (ConnectivityManager) activity
            .getSystemService(Context.CONNECTIVITY_SERVICE);
    NetworkInfo mWifi = connManager.getNetworkInfo(ConnectivityManager.TYPE_WIFI);
    if (!mWifi.isConnected()) {
        new AlertDialog.Builder(activity).setIcon(android.R.drawable.ic_dialog_alert).setTitle("Error")
                .setMessage("Wifi not connected. Application will exit.")
                .setPositiveButton("OK", new DialogInterface.OnClickListener() {
                    @Override/* w ww.  jav  a 2  s. c  o  m*/
                    public void onClick(DialogInterface dialog, int which) {
                        //activity.finish();
                    }
                }).show();
        throw new Exception("Wifi");
    }
    WifiManager wifiMgr = (WifiManager) activity.getSystemService(Activity.WIFI_SERVICE);
    WifiInfo wifiInfo = wifiMgr.getConnectionInfo();
    int ip = wifiInfo.getIpAddress();
    return String.format("%d.%d.%d.%d", (ip & 0xff), (ip >> 8 & 0xff), (ip >> 16 & 0xff), (ip >> 24 & 0xff));
}

From source file:Main.java

public static void isValidPort(String port) throws Exception {
    try {// w  ww .  j  ava 2 s .c o m
        int p = Integer.parseInt(port);
        if (p < 1 || p > 65535) {
            throw new NumberFormatException();
        }
    } catch (NumberFormatException e) {
        throw new Exception("Invalid Port Number! '" + port + "'");
    }
}

From source file:com.aerospike.load.AerospikeLoad.java

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

    Thread statPrinter = new Thread(new PrintStat(counters));
    try {/* w  w w . j  a  va  2 s.co m*/
        log.info("Aerospike loader started");
        Options options = new Options();
        options.addOption("h", "host", true, "Server hostname (default: localhost)");
        options.addOption("p", "port", true, "Server port (default: 3000)");
        options.addOption("n", "namespace", true, "Namespace (default: test)");
        options.addOption("s", "set", true, "Set name. (default: null)");
        options.addOption("c", "config", true, "Column definition file name");
        options.addOption("wt", "write-threads", true,
                "Number of writer threads (default: Number of cores * 5)");
        options.addOption("rt", "read-threads", true,
                "Number of reader threads (default: Number of cores * 1)");
        options.addOption("l", "rw-throttle", true, "Throttling of reader to writer(default: 10k) ");
        options.addOption("tt", "transaction-timeout", true,
                "write transaction timeout in miliseconds(default: No timeout)");
        options.addOption("et", "expiration-time", true,
                "Expiration time of records in seconds (default: never expire)");
        options.addOption("T", "timezone", true,
                "Timezone of source where data dump is taken (default: local timezone)");
        options.addOption("ec", "abort-error-count", true, "Error count to abort (default: 0)");
        options.addOption("wa", "write-action", true, "Write action if key already exists (default: update)");
        options.addOption("v", "verbose", false, "Logging all");
        options.addOption("u", "usage", false, "Print usage.");

        CommandLineParser parser = new PosixParser();
        CommandLine cl = parser.parse(options, args, false);

        if (args.length == 0 || cl.hasOption("u")) {
            logUsage(options);
            return;
        }

        if (cl.hasOption("l")) {
            rwThrottle = Integer.parseInt(cl.getOptionValue("l"));
        } else {
            rwThrottle = Constants.READLOAD;
        }
        // Get all command line options
        params = Utils.parseParameters(cl);

        //Get client instance
        AerospikeClient client = new AerospikeClient(params.host, params.port);
        if (!client.isConnected()) {
            log.error("Client is not able to connect:" + params.host + ":" + params.port);
            return;
        }

        if (params.verbose) {
            log.setLevel(Level.DEBUG);
        }

        // Get available processors to calculate default number of threads
        int cpus = Runtime.getRuntime().availableProcessors();
        nWriterThreads = cpus * scaleFactor;
        nReaderThreads = cpus;

        // Get writer thread count
        if (cl.hasOption("wt")) {
            nWriterThreads = Integer.parseInt(cl.getOptionValue("wt"));
            nWriterThreads = (nWriterThreads > 0
                    ? (nWriterThreads > Constants.MAX_THREADS ? Constants.MAX_THREADS : nWriterThreads)
                    : 1);
            log.debug("Using writer Threads: " + nWriterThreads);
        }
        writerPool = Executors.newFixedThreadPool(nWriterThreads);

        // Get reader thread count
        if (cl.hasOption("rt")) {
            nReaderThreads = Integer.parseInt(cl.getOptionValue("rt"));
            nReaderThreads = (nReaderThreads > 0
                    ? (nReaderThreads > Constants.MAX_THREADS ? Constants.MAX_THREADS : nReaderThreads)
                    : 1);
            log.debug("Using reader Threads: " + nReaderThreads);
        }

        String columnDefinitionFileName = cl.getOptionValue("c", null);

        log.debug("Column definition files/directory: " + columnDefinitionFileName);
        if (columnDefinitionFileName == null) {
            log.error("Column definition files/directory not specified. use -c <file name>");
            return;
        }

        File columnDefinitionFile = new File(columnDefinitionFileName);
        if (!columnDefinitionFile.exists()) {
            log.error("Column definition files/directory does not exist: "
                    + Utils.getFileName(columnDefinitionFileName));
            return;
        }

        // Get data file list
        String[] files = cl.getArgs();
        if (files.length == 0) {
            log.error("No data file Specified: add <file/dir name> to end of the command ");
            return;
        }
        List<String> allFileNames = new ArrayList<String>();
        allFileNames = Utils.getFileNames(files);
        if (allFileNames.size() == 0) {
            log.error("Given datafiles/directory does not exist");
            return;
        }
        for (int i = 0; i < allFileNames.size(); i++) {
            log.debug("File names:" + Utils.getFileName(allFileNames.get(i)));
            File file = new File(allFileNames.get(i));
            counters.write.recordTotal = counters.write.recordTotal + file.length();
        }

        //remove column definition file from list
        allFileNames.remove(columnDefinitionFileName);

        log.info("Number of data files:" + allFileNames.size());

        /**
         * Process column definition file to get meta data and bin mapping.
         */
        metadataColumnDefs = new ArrayList<ColumnDefinition>();
        binColumnDefs = new ArrayList<ColumnDefinition>();
        metadataConfigs = new HashMap<String, String>();

        if (Parser.processJSONColumnDefinitions(columnDefinitionFile, metadataConfigs, metadataColumnDefs,
                binColumnDefs, params)) {
            log.info("Config file processed.");
        } else {
            throw new Exception("Config file parsing Error");
        }

        // Add metadata of config to parameters
        String metadata;
        if ((metadata = metadataConfigs.get(Constants.INPUT_TYPE)) != null) {
            params.fileType = metadata;
            if (params.fileType.equals(Constants.CSV_FILE)) {

                // Version check
                metadata = metadataConfigs.get(Constants.VERSION);
                String[] vNumber = metadata.split("\\.");
                int v1 = Integer.parseInt(vNumber[0]);
                int v2 = Integer.parseInt(vNumber[1]);
                if ((v1 <= Constants.MajorV) && (v2 <= Constants.MinorV)) {
                    log.debug("Config version used:" + metadata);
                } else
                    throw new Exception("\"" + Constants.VERSION + ":" + metadata + "\" is not Supported");

                // Set delimiter 
                if ((metadata = metadataConfigs.get(Constants.DELIMITER)) != null && metadata.length() == 1) {
                    params.delimiter = metadata.charAt(0);
                } else {
                    log.warn("\"" + Constants.DELIMITER + ":" + metadata
                            + "\" is not properly specified in config file. Default is ','");
                }

                if ((metadata = metadataConfigs.get(Constants.IGNORE_FIRST_LINE)) != null) {
                    params.ignoreFirstLine = metadata.equals("true");
                } else {
                    log.warn("\"" + Constants.IGNORE_FIRST_LINE + ":" + metadata
                            + "\" is not properly specified in config file. Default is false");
                }

                if ((metadata = metadataConfigs.get(Constants.COLUMNS)) != null) {
                    counters.write.colTotal = Integer.parseInt(metadata);
                } else {
                    throw new Exception("\"" + Constants.COLUMNS + ":" + metadata
                            + "\" is not properly specified in config file");
                }
            } else {
                throw new Exception("\"" + params.fileType + "\" is not supported in config file");
            }
        } else {
            throw new Exception("\"" + Constants.INPUT_TYPE + "\" is not specified in config file");
        }

        // add config input to column definitions
        if (params.fileType.equals(Constants.CSV_FILE)) {
            List<String> binName = null;
            if (params.ignoreFirstLine) {
                String line;
                BufferedReader br = new BufferedReader(
                        new InputStreamReader(new FileInputStream(allFileNames.get(0)), "UTF8"));
                if ((line = br.readLine()) != null) {
                    binName = Parser.getCSVRawColumns(line, params.delimiter);
                    br.close();
                    if (binName.size() != counters.write.colTotal) {
                        throw new Exception("Number of column in config file and datafile are mismatch."
                                + " Datafile: " + Utils.getFileName(allFileNames.get(0)) + " Configfile: "
                                + Utils.getFileName(columnDefinitionFileName));
                    }
                }
            }

            //update columndefs for metadata
            for (int i = 0; i < metadataColumnDefs.size(); i++) {
                if (metadataColumnDefs.get(i).staticValue) {

                } else {
                    if (metadataColumnDefs.get(i).binValuePos < 0) {
                        if (metadataColumnDefs.get(i).columnName == null) {
                            if (metadataColumnDefs.get(i).jsonPath == null) {
                                log.error("dynamic metadata having improper info"
                                        + metadataColumnDefs.toString()); //TODO
                            } else {
                                //TODO check for json_path   
                            }
                        } else {
                            if (params.ignoreFirstLine) {
                                if (binName.indexOf(metadataColumnDefs.get(i).binValueHeader) != -1) {
                                    metadataColumnDefs.get(i).binValuePos = binName
                                            .indexOf(metadataColumnDefs.get(i).binValueHeader);
                                } else {
                                    throw new Exception("binName missing in data file:"
                                            + metadataColumnDefs.get(i).binValueHeader);
                                }
                            }
                        }
                    } else {
                        if (params.ignoreFirstLine)
                            metadataColumnDefs.get(i).binValueHeader = binName
                                    .get(metadataColumnDefs.get(i).binValuePos);
                    }
                }
                if ((!metadataColumnDefs.get(i).staticValue) && (metadataColumnDefs.get(i).binValuePos < 0)) {
                    throw new Exception("Information for bin mapping is missing in config file:"
                            + metadataColumnDefs.get(i));
                }

                if (metadataColumnDefs.get(i).srcType == null) {
                    throw new Exception(
                            "Source data type is not properly mentioned:" + metadataColumnDefs.get(i));
                }

                if (metadataColumnDefs.get(i).binNameHeader == Constants.SET
                        && !metadataColumnDefs.get(i).srcType.equals(SrcColumnType.STRING)) {
                    throw new Exception("Set name should be string type:" + metadataColumnDefs.get(i));
                }

                if (metadataColumnDefs.get(i).binNameHeader.equalsIgnoreCase(Constants.SET)
                        && params.set != null) {
                    throw new Exception(
                            "Set name is given both in config file and commandline. Provide only once.");
                }
            }

            //update columndefs for bins
            for (int i = 0; i < binColumnDefs.size(); i++) {
                if (binColumnDefs.get(i).staticName) {

                } else {
                    if (binColumnDefs.get(i).binNamePos < 0) {
                        if (binColumnDefs.get(i).columnName == null) {
                            if (binColumnDefs.get(i).jsonPath == null) {
                                log.error("dynamic bin having improper info"); //TODO
                            } else {
                                //TODO check for json_path
                            }
                        } else {
                            if (params.ignoreFirstLine) {
                                if (binName.indexOf(binColumnDefs.get(i).binNameHeader) != -1) {
                                    binColumnDefs.get(i).binNamePos = binName
                                            .indexOf(binColumnDefs.get(i).binNameHeader);
                                } else {
                                    throw new Exception("binName missing in data file:"
                                            + binColumnDefs.get(i).binNameHeader);
                                }
                            }
                        }
                    } else {
                        if (params.ignoreFirstLine)
                            binColumnDefs.get(i).binNameHeader = binName.get(binColumnDefs.get(i).binNamePos);
                    }
                }

                if (binColumnDefs.get(i).staticValue) {

                } else {
                    if (binColumnDefs.get(i).binValuePos < 0) {
                        if (binColumnDefs.get(i).columnName == null) {
                            if (binColumnDefs.get(i).jsonPath == null) {
                                log.error("dynamic bin having improper info"); //TODO
                            } else {
                                //TODO check for json_path
                            }
                        } else {
                            if (params.ignoreFirstLine) {
                                if (binName.contains(binColumnDefs.get(i).binValueHeader)) {
                                    binColumnDefs.get(i).binValuePos = binName
                                            .indexOf(binColumnDefs.get(i).binValueHeader);
                                } else if (!binColumnDefs.get(i).binValueHeader.toLowerCase()
                                        .equals(Constants.SYSTEM_TIME)) {
                                    throw new Exception("Wrong column name mentioned in config file:"
                                            + binColumnDefs.get(i).binValueHeader);
                                }
                            }
                        }
                    } else {
                        if (params.ignoreFirstLine)
                            binColumnDefs.get(i).binValueHeader = binName.get(binColumnDefs.get(i).binValuePos);
                    }

                    //check for missing entries in config file
                    if (binColumnDefs.get(i).binValuePos < 0 && binColumnDefs.get(i).binValueHeader == null) {
                        throw new Exception("Information missing(Value header or bin mapping) in config file:"
                                + binColumnDefs.get(i));
                    }

                    //check for proper data type in config file.
                    if (binColumnDefs.get(i).srcType == null) {
                        throw new Exception(
                                "Source data type is not properly mentioned:" + binColumnDefs.get(i));
                    }

                    //check for valid destination type
                    if ((binColumnDefs.get(i).srcType.equals(SrcColumnType.TIMESTAMP)
                            || binColumnDefs.get(i).srcType.equals(SrcColumnType.BLOB))
                            && binColumnDefs.get(i).dstType == null) {
                        throw new Exception("Destination type is not mentioned: " + binColumnDefs.get(i));
                    }

                    //check for encoding
                    if (binColumnDefs.get(i).dstType != null && binColumnDefs.get(i).encoding == null) {
                        throw new Exception(
                                "Encoding is not given for src-dst type conversion:" + binColumnDefs.get(i));
                    }

                    //check for valid encoding
                    if (binColumnDefs.get(i).srcType.equals(SrcColumnType.BLOB)
                            && !binColumnDefs.get(i).encoding.equals(Constants.HEX_ENCODING)) {
                        throw new Exception("Wrong encoding for blob data:" + binColumnDefs.get(i));
                    }
                }

                //Check static bin name mapped to dynamic bin value
                if ((binColumnDefs.get(i).binNamePos == binColumnDefs.get(i).binValuePos)
                        && (binColumnDefs.get(i).binNamePos != -1)) {
                    throw new Exception("Static bin name mapped to dynamic bin value:" + binColumnDefs.get(i));
                }

                //check for missing entries in config file
                if (binColumnDefs.get(i).binNameHeader == null
                        && binColumnDefs.get(i).binNameHeader.length() > Constants.BIN_NAME_LENGTH) {
                    throw new Exception("Information missing binName or large binName in config file:"
                            + binColumnDefs.get(i));
                }
            }
        }

        log.info(params.toString());
        log.debug("MetadataConfig:" + metadataColumnDefs);
        log.debug("BinColumnDefs:" + binColumnDefs);

        // Start PrintStat thread
        statPrinter.start();

        // Reader pool size
        ExecutorService readerPool = Executors.newFixedThreadPool(
                nReaderThreads > allFileNames.size() ? allFileNames.size() : nReaderThreads);
        log.info("Reader pool size : " + nReaderThreads);

        // Submit all tasks to writer threadpool.
        for (String aFile : allFileNames) {
            log.debug("Submitting task for: " + aFile);
            readerPool.submit(new AerospikeLoad(aFile, client, params));
        }

        // Wait for reader pool to complete
        readerPool.shutdown();
        log.info("Shutdown down reader thread pool");

        while (!readerPool.isTerminated())
            ;
        //readerPool.awaitTermination(20, TimeUnit.MINUTES);
        log.info("Reader thread pool terminated");

        // Wait for writer pool to complete after getting all tasks from reader pool
        writerPool.shutdown();
        log.info("Shutdown down writer thread pool");

        while (!writerPool.isTerminated())
            ;
        log.info("Writer thread pool terminated");

        // Print final statistic of aerospike-loader.
        log.info("Final Statistics of importer: (Succesfull Writes = " + counters.write.writeCount.get() + ", "
                + "Errors="
                + (counters.write.writeErrors.get() + counters.write.readErrors.get()
                        + counters.write.processingErrors.get())
                + "(" + (counters.write.writeErrors.get()) + "-Write," + counters.write.readErrors.get()
                + "-Read," + counters.write.processingErrors.get() + "-Processing)");
    } catch (Exception e) {
        log.error(e);
        if (log.isDebugEnabled()) {
            e.printStackTrace();
        }
    } finally {
        // Stop statistic printer thread.
        statPrinter.interrupt();
        log.info("Aerospike loader completed");
    }
}

From source file:Main.java

/**
 * Gets the child of the specified element having the specified unique
 * name.  If there are more than one children elements with the same name
 * and exception is thrown./*  ww w . ja  v  a2 s. c  om*/
 *
 * @param element The parent element
 * @param tagName The name of the desired child
 * @return The named child.
 * @throws Exception Child was not found or was not unique.
 */
public static Element getUniqueChild(Element element, String tagName) throws Exception {
    final Iterator goodChildren = getChildrenByTagName(element, tagName);

    if (goodChildren != null && goodChildren.hasNext()) {
        final Element child = (Element) goodChildren.next();
        if (goodChildren.hasNext()) {
            throw new Exception("expected only one " + tagName + " tag");
        }
        return child;
    } else {
        throw new Exception("expected one " + tagName + " tag");
    }
}

From source file:edu.msu.cme.rdp.seqmatch.cli.SeqmatchCheckRevSeq.java

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

    String trainingFile = null;/*  w w  w  . j a  va  2s .  c om*/
    String queryFile = null;
    String outputFile = null;
    PrintWriter revOutputWriter = new PrintWriter(System.out);
    PrintStream correctedQueryOut = System.out;
    String traineeDesc = null;
    int numOfResults = 20;
    boolean checkReverse = false;

    float diffScoreCutoff = CheckReverseSeq.DIFF_SCORE_CUTOFF;
    String format = "txt"; // default

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

        if (line.hasOption("c")) {
            checkReverse = true;
        }

        if (line.hasOption("t")) {
            trainingFile = line.getOptionValue("t");
        } else {
            throw new Exception("training file must be specified");
        }
        if (line.hasOption("q")) {
            queryFile = line.getOptionValue("q");
        } else {
            throw new Exception("query file must be specified");
        }
        if (line.hasOption("o")) {
            outputFile = line.getOptionValue("o");
        } else {
            throw new Exception("output file must be specified");
        }
        if (line.hasOption("r")) {
            revOutputWriter = new PrintWriter(line.getOptionValue("r"));
        }
        if (line.hasOption("s")) {
            correctedQueryOut = new PrintStream(line.getOptionValue("s"));
        }
        if (line.hasOption("d")) {
            diffScoreCutoff = Float.parseFloat(line.getOptionValue("d"));
        }
        if (line.hasOption("h")) {
            traineeDesc = line.getOptionValue("h");
        }
        if (line.hasOption("n")) {
            numOfResults = Integer.parseInt(line.getOptionValue("n"));
        }
        if (line.hasOption("f")) {
            format = line.getOptionValue("f");
            if (!format.equals("tab") && !format.equals("dbformat") && !format.equals("xml")) {
                throw new IllegalArgumentException("Only dbformat, tab or xml format available");
            }
        }

    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(120, "SeqmatchCheckRevSeq", "", options, "", true);
        return;
    }

    SeqmatchCheckRevSeq theObj = new SeqmatchCheckRevSeq();

    if (!checkReverse) {
        theObj.doUserLibMatch(queryFile, trainingFile, outputFile, numOfResults, format, traineeDesc);
    } else {
        theObj.checkRevSeq(queryFile, trainingFile, outputFile, revOutputWriter, correctedQueryOut,
                diffScoreCutoff, format, traineeDesc);
    }
}

From source file:Main.java

public static Document loadXMLFrom(InputStream inputStream) throws Exception {
    Document doc = null;//from w  w w.  j  ava 2  s.com
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    javax.xml.parsers.DocumentBuilder builder = null;
    try {
        builder = factory.newDocumentBuilder();
        doc = builder.parse(inputStream);
    } catch (ParserConfigurationException pce) {
        throw new Exception(pce.getMessage());
    } catch (SAXException se) {
        throw new Exception(se.getMessage());
    } catch (IOException ioe) {
        throw new Exception(ioe.getMessage());
    } finally {
        inputStream.close();
    }
    return doc;
}

From source file:com.ah.util.http.HttpFileTransferUtil.java

/**
 * upload files to ls//  w w  w  . ja v a 2  s .  c o m
 * @param fileNames -
 * @param urlParam -
 * @param delete -
 * @throws Exception -
 */
public static void uploadFilesToLS(String[] fileNames, String urlParam, boolean delete) throws Exception {

    HttpCommunication hc = uploadSettings(urlParam);

    for (String fileName : fileNames) {
        File file = new File(fileName);
        HttpResponse response = hc.uploadFile(null, file);
        if (response.getStatusLine().getStatusCode() != 200) {
            throw new Exception("Fail to upload file " + fileName + ", statuscode="
                    + response.getStatusLine().getStatusCode() + ",message="
                    + response.getStatusLine().getReasonPhrase());
        } else if (delete) {
            file.delete();
        }
    }
}

From source file:Stack.java

public void push(T item) throws Exception {
    if (top == items.length - 1)
        throw new Exception("Stack Full");
    items[++top] = item;//from   ww  w  .ja v  a 2 s. c o  m
}

From source file:edu.msu.cme.rdp.readseq.utils.SequenceTrimmer.java

public static void main(String[] args) throws IOException {
    Options options = new Options();
    options.addOption("r", "ref-seq", true,
            "Trim points are given as positions in a reference sequence from this file");
    options.addOption("i", "inclusive", false, "Trim points are inclusive");
    options.addOption("l", "length", true, "Minimum length of sequence after trimming");
    options.addOption("f", "filled-ratio", true,
            "Minimum ratio of filled model positions of sequence after trimming");
    options.addOption("o", "out", true, "Write sequences to directory (default=cwd)");
    options.addOption("s", "stats", true, "Write stats to file");

    PrintWriter statsOut = new PrintWriter(new NullWriter());
    boolean inclusive = false;
    int minLength = 0;
    int minTrimmedLength = 0;
    int maxNs = 0;
    int maxTrimNs = 0;

    int trimStart = 0;
    int trimStop = 0;
    Sequence refSeq = null;//from   w ww  .  j av  a2  s.  c om
    float minFilledRatio = 0;

    int expectedModelPos = -1;
    String[] inputFiles = null;
    File outdir = new File(".");
    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption("ref-seq")) {
            refSeq = readRefSeq(new File(line.getOptionValue("ref-seq")));
        }

        if (line.hasOption("inclusive")) {
            inclusive = true;
        }

        if (line.hasOption("length")) {
            minLength = Integer.valueOf(line.getOptionValue("length"));
        }

        if (line.hasOption("filled-ratio")) {
            minFilledRatio = Float.valueOf(line.getOptionValue("filled-ratio"));
        }

        if (line.hasOption("out")) {
            outdir = new File(line.getOptionValue("out"));
            if (!outdir.isDirectory()) {
                outdir = outdir.getParentFile();
                System.err.println("Output option is not a directory, using " + outdir + " instead");
            }
        }

        if (line.hasOption("stats")) {
            statsOut = new PrintWriter(line.getOptionValue("stats"));
        }

        args = line.getArgs();

        if (args.length < 3) {
            throw new Exception("Unexpected number of arguments");
        }

        trimStart = Integer.parseInt(args[0]);
        trimStop = Integer.parseInt(args[1]);
        inputFiles = Arrays.copyOfRange(args, 2, args.length);

        if (refSeq != null) {
            expectedModelPos = SeqUtils.getMaskedBySeqString(refSeq.getSeqString()).length();
            trimStart = translateCoord(trimStart, refSeq, CoordType.seq, CoordType.model);
            trimStop = translateCoord(trimStop, refSeq, CoordType.seq, CoordType.model);
        }

    } catch (Exception e) {
        new HelpFormatter().printHelp("SequenceTrimmer <trim start> <trim stop> <aligned file> ...", options);
        System.err.println("Error: " + e.getMessage());
    }

    System.err.println("Starting sequence trimmer");
    System.err.println("*  Input files:           " + Arrays.asList(inputFiles));
    System.err.println("*  Minimum Length:        " + minLength);
    System.err.println("*  Trim point inclusive?: " + inclusive);
    System.err.println("*  Trim points:           " + trimStart + "-" + trimStop);
    System.err.println("*  Min filled ratio:      " + minFilledRatio);
    System.err.println("*  refSeq:                "
            + ((refSeq == null) ? "model" : refSeq.getSeqName() + " " + refSeq.getDesc()));

    Sequence seq;
    SeqReader reader;
    TrimStats stats;

    writeStatsHeader(statsOut);

    FastaWriter seqWriter;
    File in;
    for (String infile : inputFiles) {
        in = new File(infile);
        reader = new SequenceReader(in);
        seqWriter = new FastaWriter(new File(outdir, "trimmed_" + in.getName()));

        while ((seq = reader.readNextSequence()) != null) {
            if (seq.getSeqName().startsWith("#")) {
                seqWriter.writeSeq(seq.getSeqName(), "", trimMetaSeq(seq.getSeqString(), trimStart, trimStop));
                continue;
            }

            stats = getStats(seq, trimStart, trimStop);
            boolean passed = didSeqPass(stats, minLength, minTrimmedLength, maxNs, maxTrimNs, minFilledRatio);
            writeStats(statsOut, seq.getSeqName(), stats, passed);
            if (passed) {
                seqWriter.writeSeq(seq.getSeqName(), seq.getDesc(), new String(stats.trimmedBases));
            }
        }

        reader.close();
        seqWriter.close();
    }

    statsOut.close();
}

From source file:Main.java

public static void isValidIP(String ip) throws Exception {
    try {/*from  www  .j  ava 2s  . c o m*/
        String[] octets = ip.split("\\.");
        for (String s : octets) {
            int i = Integer.parseInt(s);
            if (i > 255 || i < 0) {
                throw new NumberFormatException();
            }
        }
    } catch (NumberFormatException e) {
        throw new Exception("Invalid IP address! '" + ip + "'");
    }
}