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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
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/*
 * Copyright (c) 2013-2018, Centre for Genomic Regulation (CRG).
 * Copyright (c) 2013-2018, Paolo Di Tommaso and the respective authors.
 *
 *   This file is part of 'Nextflow'.
 *
 *   Nextflow is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   Nextflow is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with Nextflow.  If not, see .
 */

package nextflow.file;

/**
 * This class is almost identical to {@link java.io.ByteArrayOutputStream} with the
 * difference that methods are not synchronized
 *
 * @author Paolo Di Tommaso
 *
 * NOTE: This source has been included under the GPL "Fair Use" clause.
 * http://www.gnu.org/licenses/gpl-faq.html#GPLFairUse
 */

/*
 * Copyright (c) 1994, 2010, Oracle and/or its affiliates. All rights reserved.
 * ORACLE PROPRIETARY/CONFIDENTIAL. Use is subject to license terms.
 *
 *
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 *
 *
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 */

import java.io.IOException;
import java.io.OutputStream;
import java.io.UnsupportedEncodingException;
import java.util.Arrays;

/**
 * This class implements an output stream in which the data is
 * written into a byte array. The buffer automatically grows as data
 * is written to it.
 * The data can be retrieved using toByteArray() and
 * toString().
 * 
 * Closing a ByteArrayOutputStream has no effect. The methods in
 * this class can be called after the stream has been closed without
 * generating an IOException.
 *
 * @author  Arthur van Hoff
 * @since   JDK1.0
 */

public class FastByteArrayOutputStream extends OutputStream {

    /**
     * The buffer where data is stored.
     */
    protected byte buf[];

    /**
     * The number of valid bytes in the buffer.
     */
    protected int count;

    /**
     * Creates a new byte array output stream. The buffer capacity is
     * initially 32 bytes, though its size increases if necessary.
     */
    public FastByteArrayOutputStream() {
        this(32);
    }

    /**
     * Creates a new byte array output stream, with a buffer capacity of
     * the specified size, in bytes.
     *
     * @param   size   the initial size.
     * @exception  IllegalArgumentException if size is negative.
     */
    public FastByteArrayOutputStream(int size) {
        if (size < 0) {
            throw new IllegalArgumentException("Negative initial size: "
                    + size);
        }
        buf = new byte[size];
    }

    /**
     * Increases the capacity if necessary to ensure that it can hold
     * at least the number of elements specified by the minimum
     * capacity argument.
     *
     * @param minCapacity the desired minimum capacity
     * @throws OutOfMemoryError if {@code minCapacity < 0}.  This is
     * interpreted as a request for the unsatisfiably large capacity
     * {@code (long) Integer.MAX_VALUE + (minCapacity - Integer.MAX_VALUE)}.
     */
    private void ensureCapacity(int minCapacity) {
        // overflow-conscious code
        if (minCapacity - buf.length > 0)
            grow(minCapacity);
    }

    /**
     * Increases the capacity to ensure that it can hold at least the
     * number of elements specified by the minimum capacity argument.
     *
     * @param minCapacity the desired minimum capacity
     */
    private void grow(int minCapacity) {
        // overflow-conscious code
        int oldCapacity = buf.length;
        int newCapacity = oldCapacity << 1;
        if (newCapacity - minCapacity < 0)
            newCapacity = minCapacity;
        if (newCapacity < 0) {
            if (minCapacity < 0) // overflow
                throw new OutOfMemoryError();
            newCapacity = Integer.MAX_VALUE;
        }
        buf = Arrays.copyOf(buf, newCapacity);
    }

    /**
     * Writes the specified byte to this byte array output stream.
     *
     * @param   b   the byte to be written.
     */
    public synchronized void write(int b) {
        ensureCapacity(count + 1);
        buf[count] = (byte) b;
        count += 1;
    }

    /**
     * Writes len bytes from the specified byte array
     * starting at offset off to this byte array output stream.
     *
     * @param   b     the data.
     * @param   off   the start offset in the data.
     * @param   len   the number of bytes to write.
     */
    public synchronized void write(byte b[], int off, int len) {
        if ((off < 0) || (off > b.length) || (len < 0) ||
                ((off + len) - b.length > 0)) {
            throw new IndexOutOfBoundsException();
        }
        ensureCapacity(count + len);
        System.arraycopy(b, off, buf, count, len);
        count += len;
    }

    /**
     * Writes the complete contents of this byte array output stream to
     * the specified output stream argument, as if by calling the output
     * stream's write method using out.write(buf, 0, count).
     *
     * @param      out   the output stream to which to write the data.
     * @exception IOException  if an I/O error occurs.
     */
    public synchronized void writeTo(OutputStream out) throws IOException {
        out.write(buf, 0, count);
    }

    /**
     * Resets the count field of this byte array output
     * stream to zero, so that all currently accumulated output in the
     * output stream is discarded. The output stream can be used again,
     * reusing the already allocated buffer space.
     *
     * @see     java.io.ByteArrayInputStream#count
     */
    public synchronized void reset() {
        count = 0;
    }

    /**
     * Creates a newly allocated byte array. Its size is the current
     * size of this output stream and the valid contents of the buffer
     * have been copied into it.
     *
     * @return  the current contents of this output stream, as a byte array.
     * @see     java.io.ByteArrayOutputStream#size()
     */
    public synchronized byte toByteArray()[] {
        return Arrays.copyOf(buf, count);
    }

    /**
     * Returns the current size of the buffer.
     *
     * @return  the value of the count field, which is the number
     *          of valid bytes in this output stream.
     * @see     java.io.ByteArrayOutputStream#count
     */
    public synchronized int size() {
        return count;
    }

    /**
     * Converts the buffer's contents into a string decoding bytes using the
     * platform's default character set. The length of the new String
     * is a function of the character set, and hence may not be equal to the
     * size of the buffer.
     *
     * 
 This method always replaces malformed-input and unmappable-character
     * sequences with the default replacement string for the platform's
     * default character set. The {@linkplain java.nio.charset.CharsetDecoder}
     * class should be used when more control over the decoding process is
     * required.
     *
     * @return String decoded from the buffer's contents.
     * @since  JDK1.1
     */
    public synchronized String toString() {
        return new String(buf, 0, count);
    }

    /**
     * Converts the buffer's contents into a string by decoding the bytes using
     * the specified {@link java.nio.charset.Charset charsetName}. The length of
     * the new String is a function of the charset, and hence may not be
     * equal to the length of the byte array.
     *
     *  This method always replaces malformed-input and unmappable-character
     * sequences with this charset's default replacement string. The {@link
     * java.nio.charset.CharsetDecoder} class should be used when more control
     * over the decoding process is required.
     *
     * @param  charsetName  the name of a supported
     *              {@linkplain java.nio.charset.Charset charset}
     * @return String decoded from the buffer's contents.
     * @exception UnsupportedEncodingException
     *             If the named charset is not supported
     * @since   JDK1.1
     */
    public synchronized String toString(String charsetName)
            throws UnsupportedEncodingException
    {
        return new String(buf, 0, count, charsetName);
    }

    /**
     * Creates a newly allocated string. Its size is the current size of
     * the output stream and the valid contents of the buffer have been
     * copied into it. Each character c in the resulting string is
     * constructed from the corresponding element b in the byte
     * array such that:
     * 
     *     c == (char)(((hibyte & 0xff) << 8) | (b & 0xff))
     * 

     *
     * @deprecated This method does not properly convert bytes into characters.
     * As of JDK 1.1, the preferred way to do this is via the
     * toString(String enc) method, which takes an encoding-name
     * argument, or the toString() method, which uses the
     * platform's default character encoding.
     *
     * @param      hibyte    the high byte of each resulting Unicode character.
     * @return     the current contents of the output stream, as a string.
     * @see        java.io.ByteArrayOutputStream#size()
     * @see        java.io.ByteArrayOutputStream#toString(String)
     * @see        java.io.ByteArrayOutputStream#toString()
     */
    @Deprecated
    public synchronized String toString(int hibyte) {
        return new String(buf, hibyte, 0, count);
    }

    /**
     * Closing a ByteArrayOutputStream has no effect. The methods in
     * this class can be called after the stream has been closed without
     * generating an IOException.
     * 
     *
     */
    public void close() throws IOException {
    }

}