Example usage for java.io FileInputStream getChannel

List of usage examples for java.io FileInputStream getChannel

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Introduction

In this page you can find the example usage for java.io FileInputStream getChannel.

Prototype

public FileChannel getChannel()

Source Link

Document

Returns the unique java.nio.channels.FileChannel FileChannel object associated with this file input stream.

Usage

From source file:pyromaniac.IO.MMFastaImporter.java

/**
 * _init seq./*  w  w w . ja  v  a  2s .co m*/
 *
 * @throws Exception the exception
 */
private void _initSeq() throws Exception {
    FileInputStream tempStream = new FileInputStream(new File(this.seqFile));
    FileChannel fcSeq = tempStream.getChannel();
    this.seqSizeLong = fcSeq.size();
    this.seqStartsLL = new ArrayList<Pair<Integer, Long>>();

    for (long startPosition = 0L; startPosition < this.seqSizeLong; startPosition += HALF_GIGA) {
        MappedByteBuffer seqBuffer = fcSeq.map(FileChannel.MapMode.READ_ONLY, startPosition,
                Math.min(this.seqSizeLong - startPosition, HALF_GIGA));

        this.seqBuffers.add(seqBuffer);
        int sbf_pos = seqBuffers.size() - 1;
        int maxBuffer = 2048;
        int bufferSize = (seqBuffer.capacity() > maxBuffer) ? maxBuffer : seqBuffer.capacity();

        seqBuffer.limit(bufferSize);
        seqBuffer.position(0);

        while (seqBuffer.position() != seqBuffer.capacity()) {
            int prevPos = seqBuffer.position();
            CharBuffer result = decoder.decode(seqBuffer);
            seqBuffer.position(prevPos);

            for (int i = 0; i < result.capacity(); i++) {
                char curr = result.charAt(i);
                int posInFile = prevPos + i;

                if (curr == BEGINNING_FASTA_HEADER) {
                    seqStartsLL.add(new Pair<Integer, Long>(sbf_pos, new Long(posInFile)));
                }
            }

            int newPos = seqBuffer.limit();

            if (seqBuffer.limit() + bufferSize > seqBuffer.capacity())
                seqBuffer.limit(seqBuffer.capacity());
            else
                seqBuffer.limit(seqBuffer.limit() + bufferSize);
            seqBuffer.position(newPos);
        }
        seqBuffer.rewind();
    }

}

From source file:pyromaniac.IO.MMFastaImporter.java

/**
 * _init qual.//w w  w.j av  a  2 s.  c  o  m
 *
 * @throws Exception the exception
 */
private void _initQual() throws Exception {
    FileInputStream tempStream = new FileInputStream(new File(this.qualFile));
    FileChannel fcQual = tempStream.getChannel();
    this.qualSizeLong = fcQual.size();

    //qual starts LL contains pairs, marking file #no (in  qualBuffers) and position #no (in the buffer).
    this.qualStartsLL = new ArrayList<Pair<Integer, Long>>();

    for (long startPosition = 0L; startPosition < this.qualSizeLong; startPosition += HALF_GIGA) {
        MappedByteBuffer qualBuffer = fcQual.map(FileChannel.MapMode.READ_ONLY, startPosition,
                Math.min(this.qualSizeLong - startPosition, HALF_GIGA)); //map half a gig to this channel.
        this.qualBuffers.add(qualBuffer);
        int qbf_pos = qualBuffers.size() - 1;
        int maxBuffer = 2048;
        int bufferSize = (qualBuffer.capacity() > maxBuffer) ? maxBuffer : qualBuffer.capacity();

        qualBuffer.limit(bufferSize);
        qualBuffer.position(0);

        while (qualBuffer.position() != qualBuffer.capacity()) {
            int prevPos = qualBuffer.position();
            CharBuffer result = decoder.decode(qualBuffer);
            qualBuffer.position(prevPos);

            for (int i = 0; i < result.capacity(); i++) {
                char curr = result.charAt(i);
                int posInFile = prevPos + i;

                if (curr == BEGINNING_FASTA_HEADER) {
                    qualStartsLL.add(new Pair<Integer, Long>(qbf_pos, new Long(posInFile)));
                }
            }

            int newPos = qualBuffer.limit();

            if (qualBuffer.limit() + bufferSize > qualBuffer.capacity())
                qualBuffer.limit(qualBuffer.capacity());
            else
                qualBuffer.limit(qualBuffer.limit() + bufferSize);
            qualBuffer.position(newPos);
        }
        qualBuffer.rewind();
    }
}

From source file:filesrv.Data.java

public void writeData(ClientHandler handler) throws Exception {
    if (wrapedByteBuffer != null && wrapedByteBuffer.remaining() != 0) {
        logger.finest(nonBlockingWriteDesc);
        int written = handler.getSocketChannel().write(wrapedByteBuffer);
        logger.finest("Written " + written + " Bytes");
        if (wrapedByteBuffer.remaining() != 0) {
            handler.registerForWrite();//from ww  w . j a  va2 s.  c o m
            return;
        }
        wroteFileHttpHeader = true;
        if (sendFile == false) {
            wrapedByteBuffer = null;
            if (closeConWhenDone) {
                handler.closeConnection();
            }
            return;
        }
    }

    if (sendFile == true) {
        if (fileChannel == null) {
            File file = getFile();
            logger.finest("Sending file data: " + file);
            FileInputStream fin = new FileInputStream(file);
            fileChannel = fin.getChannel();
            fileChannel.position(startRange);
        }

        if (pooledByteBuffer == null) {
            pooledByteBuffer = (ByteBuffer) handler.getServer().getByteBufferPool().borrowObject();
        }

        if (pooledByteBuffer.hasRemaining()) {
            int ret = -1;
            long remain = fileLength - startRange;
            logger.finest("Remain: " + remain);

            if (pooledByteBuffer.remaining() > remain) {
                pooledByteBuffer.limit((int) (pooledByteBuffer.position() + remain));
            }

            ret = fileChannel.read(pooledByteBuffer);

            logger.finest("Read " + ret + " Bytes from file");
            if (ret < 0 || remain == 0) {//EOF
                fileChannel.close();
                //fileChannel = null;
            } else {
                startRange += ret;
            }
        }
        pooledByteBuffer.flip();

        if (pooledByteBuffer.hasRemaining()) {
            int written = handler.getSocketChannel().write(pooledByteBuffer);
            logger.finest("Written " + written + " Bytes to socket");
        }

        long remain = fileLength - startRange;
        if (remain == 0 && pooledByteBuffer.hasRemaining() == false) {
            fileChannel.close();
        }

        if (pooledByteBuffer.hasRemaining() == false && fileChannel.isOpen() == false) {
            sendFile = false;
            logger.finest("Sent the file!");

            if (false) {
                handler.closeConnection();
            } else {
                //so that we can take more req.
                clean();
            }
            return; //work done
        }
        pooledByteBuffer.compact(); //In case of partial write
        handler.registerForWrite();
    } //end of sendFile
}

From source file:net.librec.data.convertor.TextDataConvertor.java

/**
 * Read data from the data file. Note that we didn't take care of the
 * duplicated lines./*w w  w. ja v  a2 s .co  m*/
 *
 * @param dataColumnFormat
 *            the format of input data file
 * @param inputDataPath
 *            the path of input data file
 * @param binThold
 *            the threshold to binarize a rating. If a rating is greater
 *            than the threshold, the value will be 1; otherwise 0. To
 *            disable this appender, i.e., keep the original rating value,
 *            set the threshold a negative value
 * @throws IOException
 *            if the <code>inputDataPath</code> is not valid.
 */
private void readData(String dataColumnFormat, String inputDataPath, double binThold) throws IOException {
    LOG.info(String.format("Dataset: %s", StringUtil.last(inputDataPath, 38)));
    // Table {row-id, col-id, rate}
    Table<Integer, Integer, Double> dataTable = HashBasedTable.create();
    // Table {row-id, col-id, timestamp}
    Table<Integer, Integer, Long> timeTable = null;
    // Map {col-id, multiple row-id}: used to fast build a rating matrix
    Multimap<Integer, Integer> colMap = HashMultimap.create();
    // BiMap {raw id, inner id} userIds, itemIds
    if (this.userIds == null) {
        this.userIds = HashBiMap.create();
    }
    if (this.itemIds == null) {
        this.itemIds = HashBiMap.create();
    }
    final List<File> files = new ArrayList<File>();
    final ArrayList<Long> fileSizeList = new ArrayList<Long>();
    SimpleFileVisitor<Path> finder = new SimpleFileVisitor<Path>() {
        @Override
        public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
            fileSizeList.add(file.toFile().length());
            files.add(file.toFile());
            return super.visitFile(file, attrs);
        }
    };
    Files.walkFileTree(Paths.get(inputDataPath), finder);
    LOG.info("All dataset files " + files.toString());
    long allFileSize = 0;
    for (Long everyFileSize : fileSizeList) {
        allFileSize = allFileSize + everyFileSize.longValue();
    }
    LOG.info("All dataset files size " + Long.toString(allFileSize));
    int readingFileCount = 0;
    long loadAllFileByte = 0;
    // loop every dataFile collecting from walkFileTree
    for (File dataFile : files) {
        LOG.info("Now loading dataset file " + dataFile.toString().substring(
                dataFile.toString().lastIndexOf(File.separator) + 1, dataFile.toString().lastIndexOf(".")));
        readingFileCount += 1;
        loadFilePathRate = readingFileCount / (float) files.size();
        long readingOneFileByte = 0;
        FileInputStream fis = new FileInputStream(dataFile);
        FileChannel fileRead = fis.getChannel();
        ByteBuffer buffer = ByteBuffer.allocate(BSIZE);
        int len;
        String bufferLine = new String();
        byte[] bytes = new byte[BSIZE];
        while ((len = fileRead.read(buffer)) != -1) {
            readingOneFileByte += len;
            loadDataFileRate = readingOneFileByte / (float) fileRead.size();
            loadAllFileByte += len;
            loadAllFileRate = loadAllFileByte / (float) allFileSize;
            buffer.flip();
            buffer.get(bytes, 0, len);
            bufferLine = bufferLine.concat(new String(bytes, 0, len));
            bufferLine = bufferLine.replaceAll("\r", "\n");
            String[] bufferData = bufferLine.split("(\n)+");
            boolean isComplete = bufferLine.endsWith("\n");
            int loopLength = isComplete ? bufferData.length : bufferData.length - 1;
            for (int i = 0; i < loopLength; i++) {
                String line = new String(bufferData[i]);
                String[] data = line.trim().split("[ \t,]+");
                String user = data[0];
                String item = data[1];
                Double rate = ((dataColumnFormat.equals("UIR") || dataColumnFormat.equals("UIRT"))
                        && data.length >= 3) ? Double.valueOf(data[2]) : 1.0;

                // binarize the rating for item recommendation task
                if (binThold >= 0) {
                    rate = rate > binThold ? 1.0 : 0.0;
                }

                // inner id starting from 0
                int row = userIds.containsKey(user) ? userIds.get(user) : userIds.size();
                userIds.put(user, row);

                int col = itemIds.containsKey(item) ? itemIds.get(item) : itemIds.size();
                itemIds.put(item, col);

                dataTable.put(row, col, rate);
                colMap.put(col, row);
                // record rating's issuing time
                if (StringUtils.equals(dataColumnFormat, "UIRT") && data.length >= 4) {
                    if (timeTable == null) {
                        timeTable = HashBasedTable.create();
                    }
                    // convert to million-seconds
                    long mms = 0L;
                    try {
                        mms = Long.parseLong(data[3]); // cannot format
                        // 9.7323480e+008
                    } catch (NumberFormatException e) {
                        mms = (long) Double.parseDouble(data[3]);
                    }
                    long timestamp = timeUnit.toMillis(mms);
                    timeTable.put(row, col, timestamp);
                }
            }
            if (!isComplete) {
                bufferLine = bufferData[bufferData.length - 1];
            }
            buffer.clear();
        }
        fileRead.close();
        fis.close();
    }
    int numRows = numUsers(), numCols = numItems();
    // build rating matrix
    preferenceMatrix = new SparseMatrix(numRows, numCols, dataTable, colMap);
    if (timeTable != null)
        datetimeMatrix = new SparseMatrix(numRows, numCols, timeTable, colMap);
    // release memory of data table
    dataTable = null;
    timeTable = null;
}

From source file:esg.node.components.monitoring.MonitorDAO.java

private void loadDiskInfoResource() {
    disk_info_dsroot_pat = Pattern.compile("thredds_dataset_roots\\s*=\\s*(.*?)\\s*\\w+\\s*?=");
    disk_info_dsroot_keyval_pat = Pattern.compile("\\s*(\\w+)\\s*\\|\\s*(\\S+)\\s*");

    String filename = props.getProperty("monitor.esg.ini",
            System.getenv().get("ESG_USER_HOME") + "/.esgcet/esg.ini");
    File iniFile = new File(filename);
    if (!iniFile.exists()) {
        log.warn("ESG publisher config file [" + filename + "] not found! Cannot provide disk info!");
        return;/* w w w.  j  av  a2  s  . c  o m*/
    }

    log.debug("Scanning for drives specified in: " + filename);

    try {
        FileInputStream fis = new FileInputStream(iniFile);
        FileChannel fc = fis.getChannel();
        disk_info_byte_buffer = fc.map(FileChannel.MapMode.READ_ONLY, 0, (int) fc.size());
    } catch (FileNotFoundException e) {
        log.error(e);
    } catch (IOException e) {
        log.error(e);
    }
}

From source file:com.wwpass.connection.WWPassConnection.java

private static PKCS8EncodedKeySpec readKeyFile(String path) throws IOException {
    FileInputStream stream = new FileInputStream(new File(path));
    try {//from  www.j  a  v a 2s. c o m
        FileChannel fc = stream.getChannel();
        MappedByteBuffer bb = fc.map(FileChannel.MapMode.READ_ONLY, 0, fc.size());
        String pem = Charset.defaultCharset().decode(bb).toString();
        pem = pem.replaceFirst("-----BEGIN (RSA )?PRIVATE KEY-----\r?\n?", "")
                .replace("-----END (RSA )?PRIVATE KEY-----", "");
        Base64 dec1 = new Base64();
        byte[] encoded = dec1.decode(pem);
        return new PKCS8EncodedKeySpec(encoded);
    } finally {
        stream.close();
    }
}

From source file:edu.harvard.iq.dvn.core.analysis.NetworkDataServiceBean.java

private void copyFile(StudyFileEditBean editBean) throws IOException {
    File tempFile = new File(editBean.getTempSystemFileLocation());
    dbgLog.fine("begin copyFile()");
    // create a sub-directory "ingested"
    File newDir = new File(tempFile.getParentFile(), "ingested");

    if (!newDir.exists()) {
        newDir.mkdirs();/*  w w w. jav a2  s .  c o m*/
    }
    dbgLog.fine("newDir: abs path:\n" + newDir.getAbsolutePath());

    File newFile = new File(newDir, tempFile.getName());

    FileInputStream fis = new FileInputStream(tempFile);
    FileOutputStream fos = new FileOutputStream(newFile);
    FileChannel fcin = fis.getChannel();
    FileChannel fcout = fos.getChannel();
    fcin.transferTo(0, fcin.size(), fcout);
    fcin.close();
    fcout.close();
    fis.close();
    fos.close();

    dbgLog.fine("newFile: abs path:\n" + newFile.getAbsolutePath());

    // store the tab-file location
    editBean.setIngestedSystemFileLocation(newFile.getAbsolutePath());

}

From source file:com.android.mms.transaction.NotificationTransaction.java

public int checkPduResult() {
    if (!mPduFile.exists()) {
        Log.e(MmsApp.TXN_TAG, "checkPduResult MMS Fail, no pduFile = " + mPduFile);
        return SmsManager.MMS_ERROR_UNSPECIFIED;
    }//  w w  w .  ja  v a 2s. co m
    FileChannel channel = null;
    FileInputStream fs = null;
    RetrieveConf retrieveConf;
    try {
        fs = new FileInputStream(mPduFile);
        channel = fs.getChannel();
        ByteBuffer byteBuffer = ByteBuffer.allocate((int) channel.size());
        while ((channel.read(byteBuffer)) > 0) {
            // do nothing
            // System.out.println("reading");
        }
        final GenericPdu pdu = (new PduParser(byteBuffer.array(),
                PduParserUtil.shouldParseContentDisposition(mSubId))).parse();
        if (pdu == null || !(pdu instanceof RetrieveConf)) {
            Log.e(MmsApp.TXN_TAG, "checkPduResult: invalid parsed PDU");
            return SmsManager.MMS_ERROR_UNSPECIFIED;
        }
        retrieveConf = (RetrieveConf) pdu;

        // Store the downloaded message
        PduPersister persister = PduPersister.getPduPersister(mContext);
        Uri messageUri = persister.persist(pdu, Telephony.Mms.Inbox.CONTENT_URI, true/*createThreadId*/,
                true/*groupMmsEnabled*/, null/*preOpenedFiles*/);
        if (messageUri == null) {
            Log.e(MmsApp.TXN_TAG, "checkPduResult: can not persist message");
            return SmsManager.MMS_ERROR_UNSPECIFIED;
        }
        mMessageUri = messageUri.toString();
        // Update some of the properties of the message
        final ContentValues values = new ContentValues();
        values.put(Telephony.Mms.DATE, System.currentTimeMillis() / 1000L);
        values.put(Telephony.Mms.READ, 0);
        values.put(Telephony.Mms.SEEN, 0);
        String creator = ActivityThread.currentPackageName();
        if (!TextUtils.isEmpty(creator)) {
            values.put(Telephony.Mms.CREATOR, creator);
        }
        values.put(Telephony.Mms.SUBSCRIPTION_ID, mSubId);
        if (SqliteWrapper.update(mContext, mContext.getContentResolver(), messageUri, values, null/*where*/,
                null/*selectionArg*/) != 1) {
            Log.e(MmsApp.TXN_TAG, "persistIfRequired: can not update message");
        }
        // Delete the corresponding NotificationInd
        SqliteWrapper.delete(mContext, mContext.getContentResolver(), Telephony.Mms.CONTENT_URI,
                LOCATION_SELECTION,
                new String[] { Integer.toString(PduHeaders.MESSAGE_TYPE_NOTIFICATION_IND), mContentLocation });
        return Activity.RESULT_OK;
    } catch (IOException e) {
        e.printStackTrace();
        return SmsManager.MMS_ERROR_UNSPECIFIED;
    } catch (MmsException e) {
        e.printStackTrace();
        return SmsManager.MMS_ERROR_UNSPECIFIED;
    } catch (SQLiteException e) {
        e.printStackTrace();
        return SmsManager.MMS_ERROR_UNSPECIFIED;
    } catch (RuntimeException e) {
        e.printStackTrace();
        return SmsManager.MMS_ERROR_UNSPECIFIED;
    } finally {
        if (mPduFile != null) {
            mPduFile.delete();
        }
        try {
            if (channel != null) {
                channel.close();
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
        try {
            if (fs != null) {
                fs.close();
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

From source file:dk.netarkivet.common.utils.FileUtils.java

/**
 * Copy file from one location to another. Will silently overwrite an
 * already existing file.//from w w  w  . ja va2  s.  co m
 *
 * @param from
 *            original to copy
 * @param to
 *            destination of copy
 * @throws IOFailure if an io error occurs while copying file,
 * or the original file does not exist.
 */
public static void copyFile(File from, File to) {
    ArgumentNotValid.checkNotNull(from, "File from");
    ArgumentNotValid.checkNotNull(to, "File to");
    if (!from.exists()) {
        String errMsg = "Original file '" + from.getAbsolutePath() + "' does not exist";
        log.warn(errMsg);
        throw new IOFailure(errMsg);
    }
    try {
        FileInputStream inStream = null;
        FileOutputStream outStream = null;
        FileChannel in = null;
        FileChannel out = null;
        try {
            inStream = new FileInputStream(from);
            outStream = new FileOutputStream(to);
            in = inStream.getChannel();
            out = outStream.getChannel();
            long bytesTransferred = 0;
            do {
                //Note: in.size() is called every loop, because if it should
                //change size, we might end up in an infinite loop trying to
                //copy more bytes than are actually available.
                bytesTransferred += in.transferTo(bytesTransferred,
                        Math.min(Constants.IO_CHUNK_SIZE, in.size() - bytesTransferred), out);
            } while (bytesTransferred < in.size());
        } finally {
            if (inStream != null) {
                inStream.close();
            }
            if (outStream != null) {
                outStream.close();
            }
            if (in != null) {
                in.close();
            }
            if (out != null) {
                out.close();
            }
        }
    } catch (IOException e) {
        final String errMsg = "Error copying file '" + from.getAbsolutePath() + "' to '" + to.getAbsolutePath()
                + "'";
        log.warn(errMsg, e);
        throw new IOFailure(errMsg, e);
    }
}

From source file:org.apache.hadoop.hdfs.client.ShortCircuitReplica.java

public ShortCircuitReplica(ExtendedBlockId key, FileInputStream dataStream, FileInputStream metaStream,
        ShortCircuitCache cache, long creationTimeMs, Slot slot) throws IOException {
    this.key = key;
    this.dataStream = dataStream;
    this.metaStream = metaStream;
    this.metaHeader = BlockMetadataHeader.preadHeader(metaStream.getChannel());
    if (metaHeader.getVersion() != 1) {
        throw new IOException(
                "invalid metadata header version " + metaHeader.getVersion() + ".  Can only handle version 1.");
    }/*  w w  w  .  j  a v a  2s .  c  o  m*/
    this.cache = cache;
    this.creationTimeMs = creationTimeMs;
    this.slot = slot;
}