Example usage for java.io RandomAccessFile seek

Introduction

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

Prototype

public void seek(long pos) throws IOException 

Source Link

Document

Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.

Usage

From source file:org.broadinstitute.gatk.utils.io.IOUtils.java

/**
 * Determines the uncompressed size of a GZIP file. Uses the GZIP ISIZE field in the last
 * 4 bytes of the file to get this information.
 *
 * @param gzipFile GZIP-format file whose uncompressed size to determine
 * @return The uncompressed size (in bytes) of the GZIP file
 *///  w w w  .  j  av a 2s  .co m
public static int getGZIPFileUncompressedSize(File gzipFile) {
    if (gzipFile == null) {
        throw new ReviewedGATKException("GZIP file to examine was null");
    }

    try {
        // The GZIP ISIZE field holds the uncompressed size of the compressed data.
        // It occupies the last 4 bytes of any GZIP file:
        RandomAccessFile in = new RandomAccessFile(gzipFile, "r");
        in.seek(gzipFile.length() - 4);
        byte[] sizeBytes = new byte[4];
        in.read(sizeBytes, 0, 4);

        ByteBuffer byteBuf = ByteBuffer.wrap(sizeBytes);
        byteBuf.order(ByteOrder.LITTLE_ENDIAN); // The GZIP spec mandates little-endian byte order
        int uncompressedSize = byteBuf.getInt();

        // If the size read in is negative, we've overflowed our signed integer:
        if (uncompressedSize < 0) {
            throw new UserException.CouldNotReadInputFile(String.format(
                    "Cannot accurately determine the uncompressed size of file %s "
                            + "because it's either larger than %d bytes or the GZIP ISIZE field is corrupt",
                    gzipFile.getAbsolutePath(), Integer.MAX_VALUE));
        }

        return uncompressedSize;
    } catch (IOException e) {
        throw new UserException.CouldNotReadInputFile(gzipFile, e);
    }
}

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From source file:org.broadinstitute.sting.utils.io.IOUtils.java

/**
 * Determines the uncompressed size of a GZIP file. Uses the GZIP ISIZE field in the last
 * 4 bytes of the file to get this information.
 *
 * @param gzipFile GZIP-format file whose uncompressed size to determine
 * @return The uncompressed size (in bytes) of the GZIP file
 *//*from  www .  j  ava2s . co m*/
public static int getGZIPFileUncompressedSize(File gzipFile) {
    if (gzipFile == null) {
        throw new ReviewedStingException("GZIP file to examine was null");
    }

    try {
        // The GZIP ISIZE field holds the uncompressed size of the compressed data.
        // It occupies the last 4 bytes of any GZIP file:
        RandomAccessFile in = new RandomAccessFile(gzipFile, "r");
        in.seek(gzipFile.length() - 4);
        byte[] sizeBytes = new byte[4];
        in.read(sizeBytes, 0, 4);

        ByteBuffer byteBuf = ByteBuffer.wrap(sizeBytes);
        byteBuf.order(ByteOrder.LITTLE_ENDIAN); // The GZIP spec mandates little-endian byte order
        int uncompressedSize = byteBuf.getInt();

        // If the size read in is negative, we've overflowed our signed integer:
        if (uncompressedSize < 0) {
            throw new UserException.CouldNotReadInputFile(String.format(
                    "Cannot accurately determine the uncompressed size of file %s "
                            + "because it's either larger than %d bytes or the GZIP ISIZE field is corrupt",
                    gzipFile.getAbsolutePath(), Integer.MAX_VALUE));
        }

        return uncompressedSize;
    } catch (IOException e) {
        throw new UserException.CouldNotReadInputFile(gzipFile, e);
    }
}

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From source file:com.ettrema.zsync.UploadReader.java

/**
 * Reads a number of bytes from the InputStream equal to the size of the specified Range and
 * writes them into that Range of the RandomAccessFile.
 * /*www.  ja v  a2s  .  com*/
 * @param dataIn The InputStream containing the data to be copied
 * @param range The target location in the RandomAccessFile
 * @param buffer A byte array used to transfer data from dataIn to fileOut
 * @param fileOut A RandomAccessFile for the File being assembled
 * @throws IOException
 */
private static void sendBytes(InputStream dataIn, Range range, byte[] buffer, RandomAccessFile fileOut)
        throws IOException {

    long bytesLeft = (range.getFinish() - range.getStart());
    int bytesRead = 0;
    int readAtOnce = 0;

    fileOut.seek(range.getStart());

    while (bytesLeft > 0) {

        readAtOnce = (int) Math.min(buffer.length, bytesLeft);
        bytesRead = dataIn.read(buffer, 0, readAtOnce);
        fileOut.write(buffer, 0, bytesRead);
        bytesLeft -= bytesRead;

        if (bytesLeft > 0 && bytesRead < 0) {

            throw new RuntimeException("Unable to copy byte Range: " + range.getRange()
                    + ". End of InputStream reached with " + bytesLeft + " bytes left.");
        }
    }
}

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From source file:org.apache.hadoop.dfs.TestDatanodeBlockScanner.java

public static boolean corruptReplica(String blockName, int replica) throws IOException {
    Random random = new Random();
    File baseDir = new File(System.getProperty("test.build.data"), "dfs/data");
    boolean corrupted = false;
    for (int i = replica * 2; i < replica * 2 + 2; i++) {
        File blockFile = new File(baseDir, "data" + (i + 1) + "/current/" + blockName);
        if (blockFile.exists()) {
            // Corrupt replica by writing random bytes into replica
            RandomAccessFile raFile = new RandomAccessFile(blockFile, "rw");
            FileChannel channel = raFile.getChannel();
            String badString = "BADBAD";
            int rand = random.nextInt((int) channel.size() / 2);
            raFile.seek(rand);
            raFile.write(badString.getBytes());
            raFile.close();/*from www  . ja  va 2s .  co  m*/
            corrupted = true;
        }
    }
    return corrupted;
}

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From source file:dk.netarkivet.common.utils.cdx.BinSearch.java

/** Perform a binary search for a string in a file.
 * Returns the position of a line that begins with 'find'.
 * Note that this may not be the first line, if there be duplicates.
 * @param in the RandomAccessFile/*  w w w  .j a  va  2 s . c o m*/
 * @param find The String to look for in the above file
 * @throws IOException If some I/O error occurs
 * @return The index of a line matching find, or -1 if none found.
 */
private static long binSearch(RandomAccessFile in, String find) throws IOException {
    // The starting position for the binary search.  Always
    // at the start of a line that's < the wanted line.
    long startpos = 0;
    // Ensure that startpos isn't a match.
    in.seek(startpos);
    String line = in.readLine();
    if (line == null) {
        return -1;
    }
    if (compare(line, find) == 0) {
        return startpos;
    }
    // The ending position for the binary search.  Always
    // *after* a line that >= the wanted line (which also means
    // at the start of a line that's > the wanted line, or at EOF
    long endpos = in.length();

    // Set file pos to first line after middle.
    findMiddleLine(in, startpos, endpos);

    // When done searching, midpos points to a matching line, if any
    // Until the search is done, both endpos and startpos point
    // at non-matching lines (or EOF), and startpos < prevpos < endpos
    long prevpos = in.getFilePointer();
    do {
        line = in.readLine();
        if (line == null) {
            log.debug("Internal: Ran past end of file in '" + in + "' at " + endpos);
            return -1;
        }
        int cmp = compare(line, find);
        if (cmp > 0) {
            endpos = prevpos;
        } else if (cmp < 0) {
            startpos = prevpos;
        } else {
            return prevpos;
        }
        if (startpos == endpos) {
            return -1;
        }
        prevpos = findMiddleLine(in, startpos, endpos);
        if (prevpos == -1) {
            return -1;
        }
    } while (true);
}

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From source file:jsave.Utils.java

public static final void align_32(RandomAccessFile raf) throws IOException {
    long pos = raf.getFilePointer();
    if (pos % 4 != 0) {
        raf.seek(pos + 4 - pos % 4);
    }/*from   w ww  .j  ava2s . c o m*/
}

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From source file:org.gcaldaemon.core.sendmail.SendMail.java

private static final String readContent(RandomAccessFile raf) throws Exception {
    String content = null;/* www.ja v  a  2  s  . c o m*/
    int len = Math.min((int) raf.length(), 500);
    byte[] bytes = new byte[len];
    raf.seek(0);
    raf.readFully(bytes);
    if (bytes[0] == -17 && bytes[1] == -69 && bytes[2] == -65) {

        // UTF-8 header found
        log.debug("File encoding is 'UTF-8'.");
        bytes = new byte[(int) raf.length() - 3];
        raf.seek(3);
        raf.readFully(bytes);
        content = StringUtils.decodeToString(bytes, StringUtils.UTF_8).trim();
    } else {

        // Autodetect encoding
        String header = StringUtils.decodeToString(bytes, StringUtils.US_ASCII).toUpperCase().replace(':', '=');
        String encoding = null;
        int pos = header.indexOf("ENCODING=");
        if (pos != -1) {
            int end = endOf(header, pos + 10);
            if (end != -1) {
                encoding = header.substring(pos + 9, end);
                encoding = encoding.replace('\'', ' ');
                encoding = encoding.replace('\"', ' ');
                encoding = encoding.trim();
            }
        }

        // Check XML-encoding
        if (encoding == null) {
            pos = header.indexOf("CHARSET=");
            if (pos != -1) {
                int end = endOf(header, pos + 10);
                if (end != -1) {
                    encoding = header.substring(pos + 8, end);
                    encoding = encoding.replace('\'', ' ');
                    encoding = encoding.replace('\"', ' ');
                    encoding = encoding.trim();
                }
            }
        }

        // Convert file encoding to Java encoding
        if (encoding == null) {
            encoding = Charset.defaultCharset().name();
        } else {
            if (encoding.equals("UTF8")) {
                encoding = StringUtils.UTF_8;
            }
        }
        log.debug("File encoding is '" + encoding + "'.");
        bytes = new byte[(int) raf.length()];
        raf.seek(0);
        raf.readFully(bytes);
        content = StringUtils.decodeToString(bytes, encoding).trim();
    }
    return content;
}

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From source file:phex.util.FileUtils.java

/**
 * Splits the source file at the splitpoint into the destination file.
 * The result will be the source file containing data to the split point and
 * the destination file containing the data from the split point to the end
 * of the file.//from  w w w .j a  v  a  2s .  c  om
 *
 * @param source      the source file to split.
 * @param destination the destination file to split into.
 * @param splitPoint  the split point byte position inside the file.
 *                    When the file size is 10 and the splitPoint is 3 the source file will contain
 *                    the first 3 bytes while the destination file will contain the last 7 bytes.
 * @throws IOException in case of a IOException during split operation.
 */
public static void splitFile(File source, File destination, long splitPoint) throws IOException {
    // open files
    RandomAccessFile sourceFile = new RandomAccessFile(source, "rws");
    try {
        FileOutputStream outStream = new FileOutputStream(destination);
        try {
            sourceFile.seek(splitPoint);
            byte[] buffer = new byte[(int) Math.min(BUFFER_LENGTH, source.length() + 1)];
            int length;
            while (-1 != (length = sourceFile.read(buffer))) {
                outStream.write(buffer, 0, length);
            }
            sourceFile.setLength(splitPoint);
        } finally {
            IOUtil.closeQuietly(outStream);
        }
    } finally {
        IOUtil.closeQuietly(sourceFile);
    }
}

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From source file:org.apache.storm.utils.ServerUtils.java

/**
 * Given a zip File input it will return its size
 * Only works for zip files whose uncompressed size is less than 4 GB,
 * otherwise returns the size module 2^32, per gzip specifications
 * @param myFile The zip file as input//from www .ja v  a2  s  .c o m
 * @throws IOException
 * @return zip file size as a long
 */
public static long zipFileSize(File myFile) throws IOException {
    RandomAccessFile raf = new RandomAccessFile(myFile, "r");
    raf.seek(raf.length() - 4);
    long b4 = raf.read();
    long b3 = raf.read();
    long b2 = raf.read();
    long b1 = raf.read();
    long val = (b1 << 24) | (b2 << 16) + (b3 << 8) + b4;
    raf.close();
    return val;
}

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From source file:eionet.eunis.servlets.DownloadServlet.java

/**
 * Copy the given byte range of the given input to the given output.
 *
 * @param input The input to copy the given range to the given output for.
 * @param output The output to copy the given range from the given input for.
 * @param start Start of the byte range.
 * @param length Length of the byte range.
 * @throws IOException If something fails at I/O level.
 */// w ww  . ja  v  a 2s .c o  m
private static void copy(RandomAccessFile input, OutputStream output, long start, long length)
        throws IOException {
    byte[] buffer = new byte[DEFAULT_BUFFER_SIZE];
    int read;

    if (input.length() == length) {
        // Write full range.
        while ((read = input.read(buffer)) > 0) {
            output.write(buffer, 0, read);
        }
    } else {
        // Write partial range.
        input.seek(start);
        long toRead = length;

        while ((read = input.read(buffer)) > 0) {
            toRead = toRead - read;
            if (toRead > 0) {
                output.write(buffer, 0, read);
            } else {
                output.write(buffer, 0, (int) toRead + read);
                break;
            }
        }
    }
}

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