/*
 * The MIT License
 *
 * Copyright (c) 2009 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package htsjdk.samtools.util;

import java.io.ByteArrayInputStream;
import java.io.Closeable;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.SyncFailedException;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;

/**
 * Encapsulates file representation of various primitive data types.  Forces little-endian disk representation.
 * Note that this class is currently not very efficient.  There are plans to increase the size of the ByteBuffer,
 * and move data between the ByteBuffer and the underlying input or output stream in larger chunks.
 *
 * All the read methods throw RuntimeEOFException if the input stream is exhausted before the required number
 * of bytes are read.
 *
 * @author Dave Tefft
 */
public class BinaryCodec implements Closeable {

    //Outstream to write to
    private OutputStream outputStream;
    //If a file or filename was given it will be stored here.  Used for error reporting.
    private String outputFileName;

    //Input stream to read from
    private InputStream inputStream;
    //If a file or filename was give to read from it will be stored here.  Used for error reporting.
    private String inputFileName;

    /*
    Mode that the BinaryCodec is in.  It is either writing to a binary file or reading from.
    This is set to true if it is writing to a binary file
    Right now we don't support reading and writing to the same file with the same BinaryCodec instance
    */
    private boolean isWriting;

    /**
     * For byte swapping.
     */
    private ByteBuffer byteBuffer;

    /**
     * For reading Strings of known length, this can reduce object creation
     */
    private final byte[] scratchBuffer = new byte[16];

    // Byte order used in BAM files.
    private static final ByteOrder LITTLE_ENDIAN = ByteOrder.LITTLE_ENDIAN;
    private static final byte NULL_BYTE[] = {0};

    private static final long MAX_UBYTE = (Byte.MAX_VALUE * 2) + 1;
    private static final long MAX_USHORT = (Short.MAX_VALUE * 2) + 1;
    private static final long MAX_UINT = ((long)Integer.MAX_VALUE * 2) + 1;

    // We never serialize more than this much at a time (except for Strings)
    private static final int MAX_BYTE_BUFFER = 8;

    //////////////////////////////////////////////////
    // Constructors                                 //
    //////////////////////////////////////////////////

    /**
     * Constructs BinaryCodec from a file and set it's mode to writing or not
     *
     * @param file    file to be written to or read from
     * @param writing whether the file is being written to
     */
    public BinaryCodec(final File file, final boolean writing) {
        this();
        try {
            this.isWriting = writing;
            if (this.isWriting) {
                this.outputStream = new FileOutputStream(file);
                this.outputFileName = file.getName();
            } else {
                this.inputStream = new FileInputStream(file);
                this.inputFileName = file.getName();
            }
        } catch (FileNotFoundException e) {
            throw new RuntimeIOException("File not found: " + file, e);
        }
    }

    /**
     * Constructs BinaryCodec from a file name and set it's mode to writing or not
     *
     * @param fileName name of the file to be written to or read from
     * @param writing  writing whether the file is being written to
     */
    public BinaryCodec(final String fileName, final boolean writing) {
        this(new File(fileName), writing);
    }

    /**
     * Constructs BinaryCodec from an output stream
     *
     * @param outputStream Stream to write to, since it's an output stream we know that isWriting
     *                     should be set to true
     */
    public BinaryCodec(final OutputStream outputStream) {
        this();
        setOutputStream(outputStream);
    }

    /**
     * Constructs BinaryCodec from an input stream
     *
     * @param inputStream Stream to read from, since we are reading isWriting is set to false
     */
    public BinaryCodec(final InputStream inputStream) {
        this();
        setInputStream(inputStream);
    }

    /**
     * Ambiguous whether reading or writing until set{In,Out}putStream is called
     */
    public BinaryCodec() {
        initByteBuffer();
    }

    /**
     * Shared among ctors.
     * Note that if endianness is changed, all the unsigned methods must also be changed.
     */
    private void initByteBuffer() {
        byteBuffer = ByteBuffer.allocate(MAX_BYTE_BUFFER);
        byteBuffer.order(LITTLE_ENDIAN);
    }

    //////////////////////////////////////////////////
    // Writing methods                              //
    //////////////////////////////////////////////////


    /**
     * Write whatever has been put into the byte buffer
     * @param numBytes -- how much to write.  Note that in case of writing an unsigned value,
     * more bytes were put into the ByteBuffer than will get written out.
     */
    private void writeByteBuffer(final int numBytes) {
        assert(numBytes <= byteBuffer.limit());
        writeBytes(byteBuffer.array(), 0, numBytes);
    }

    /**
     * Writes a byte to the output buffer
     *
     * @param bite byte array to write
     */
    public void writeByte(final byte bite) {
        byteBuffer.clear();
        byteBuffer.put(bite);
        writeByteBuffer(1);
    }

    public void writeByte(final int b) {
        writeByte((byte)b);
    }

    /**
     * Writes a byte array to the output buffer
     *
     * @param bytes value to write
     */
    public void writeBytes(final byte[] bytes) {
        writeBytes(bytes,  0, bytes.length);
    }

    public void writeBytes(final byte[] bytes, final int startOffset, final int numBytes) {
        if (!isWriting) {
            throw new IllegalStateException("Calling write method on BinaryCodec open for read.");
        }
        try {
            outputStream.write(bytes, startOffset, numBytes);
        } catch (IOException e) {
            throw new RuntimeIOException(constructErrorMessage("Write error"), e);
        }
    }

    /**
     * Write a 32-bit int to the output stream
     *
     * @param value int to write
     */
    public void writeInt(final int value) {
        byteBuffer.clear();
        byteBuffer.putInt(value);
        writeByteBuffer(4);
    }

    /**
     * Write a double (8 bytes) to the output stream
     *
     * @param value double to write
     */
    public void writeDouble(final double value) {
        byteBuffer.clear();
        byteBuffer.putDouble(value);
        writeByteBuffer(8);
    }

    /**
     * Write a 64-bit long to the output stream
     *
     * @param value long to write
     */
    public void writeLong(final long value) {
        byteBuffer.clear();
        byteBuffer.putLong(value);
        writeByteBuffer(8);
    }


    /**
     * Write a 16-bit short to output stream
     */
    public void writeShort(final short value) {
        byteBuffer.clear();
        byteBuffer.putShort(value);
        writeByteBuffer(2);
    }

    /**
     * Write a float (4 bytes) to the output stream
     *
     * @param value float to write
     */
    public void writeFloat(final float value) {
        byteBuffer.clear();
        byteBuffer.putFloat(value);
        writeByteBuffer(4);
    }

    /**
     * Writes a boolean (1 byte) to the output buffer
     *
     * @param value boolean to write
     */
    public void writeBoolean(final boolean value) {
        byteBuffer.clear();
        byteBuffer.put(value ? (byte)1 : (byte)0);
        writeByteBuffer(1);
    }

    /**
     * Writes a string to the buffer as ASCII bytes
     *
     * @param value       string to write to buffer
     * @param writeLength prefix the string with the length as a 32-bit int
     * @param appendNull  add a null byte to the end of the string
     */
    public void writeString(final String value, final boolean writeLength, final boolean appendNull) {
        if (writeLength) {
            int lengthToWrite = value.length();
            if (appendNull) lengthToWrite++;
            writeInt(lengthToWrite);
        }

        //Actually writes the string to a buffer
        writeString(value);

        if (appendNull) writeBytes(NULL_BYTE);

    }


    /**
     * Write a string to the buffer as ASCII bytes
     *
     * @param value string to write
     */
    private void writeString(final String value) {
        writeBytes(StringUtil.stringToBytes(value));
    }

    /**
     * Write an 8-bit unsigned byte.
     * NOTE: This method will break if we change to big-endian.
     */
    public void writeUByte(final short val) {
        if (val < 0) {
            throw new IllegalArgumentException("Negative value (" + val + ") passed to unsigned writing method.");
        }
        if (val > MAX_UBYTE) {
            throw new IllegalArgumentException("Value (" + val + ") to large to be written as ubyte.");
        }
        byteBuffer.clear();
        byteBuffer.putShort(val);
        writeByteBuffer(1);
    }

    /**
     * Write a 16-bit unsigned short.
     * NOTE: This method will break if we change to big-endian.
     */
    public void writeUShort(final int val) {
        if (val < 0) {
            throw new IllegalArgumentException("Negative value (" + val + ") passed to unsigned writing method.");
        }
        if (val > MAX_USHORT) {
            throw new IllegalArgumentException("Value (" + val + ") too large to be written as ushort.");
        }
        byteBuffer.clear();
        byteBuffer.putInt(val);
        writeByteBuffer(2);
    }

    /**
     * Write a 32-bit unsigned int.
     * NOTE: This method will break if we change to big-endian.
     */
    public void writeUInt(final long val) {
        if (val < 0) {
            throw new IllegalArgumentException("Negative value (" + val + ") passed to unsigned writing method.");
        }
        if (val > MAX_UINT) {
            throw new IllegalArgumentException("Value (" + val + ") to large to be written as uint.");
        }
        byteBuffer.clear();
        byteBuffer.putLong(val);
        writeByteBuffer(4);
    }

    //////////////////////////////////////////////////
    // Reading methods                              //
    //////////////////////////////////////////////////

    /**
     * Read a byte array from the input stream.
     *
     * @throws htsjdk.samtools.util.RuntimeEOFException if fewer than buffer.length bytes to read
     */
    public void readBytes(final byte[] buffer) {
        readBytes(buffer, 0, buffer.length);
    }

    /**
     * Read a byte array from the input stream
     *
     * @param buffer where to put bytes read
     * @param offset offset to start putting bytes into buffer
     * @param length number of bytes to read
     * @throws RuntimeEOFException if fewer than length bytes to read
     */
    public void readBytes(final byte[] buffer, final int offset, final int length) {
        int totalNumRead = 0;
        do {
            final int numRead = readBytesOrFewer(buffer, offset + totalNumRead, length - totalNumRead);
            if (numRead < 0) {
                String msg = String.format("Premature EOF. Expected %d but only received %d", length, totalNumRead);
                throw new RuntimeEOFException(constructErrorMessage(msg));
            } else {
                totalNumRead += numRead;
            }
        } while (totalNumRead < length);
    }

    /**
     * Reads a byte array from the input stream.
     *
     * @param buffer where to put bytes read
     * @param offset offset to start putting bytes into buffer
     * @param length number of bytes to read.  Fewer bytes may be read if EOF is reached before length bytes
     *        have been read.
     * @return the total number of bytes read into the buffer, or -1 if there is no more data because the end of the stream has been reached.
     */
    public int readBytesOrFewer(final byte[] buffer, final int offset, final int length) {
        if (isWriting) {
            throw new IllegalStateException("Calling read method on BinaryCodec open for write.");
        }
        try {
            return inputStream.read(buffer, offset, length);
        } catch (IOException e) {
            throw new RuntimeIOException(constructErrorMessage("Read error"), e);
        }
    }

    /**
     * @return a single byte read from the input stream.
     */
    public byte readByte() {
        if (isWriting) {
            throw new IllegalStateException("Calling read method on BinaryCodec open for write.");
        }
        try {
            final int ret = inputStream.read();
            if (ret == -1) {
                throw new RuntimeEOFException(constructErrorMessage("Premature EOF"));
            }
            return (byte)ret;
        } catch (IOException e) {
            throw new RuntimeIOException(constructErrorMessage("Read error"), e);
        }
    }

    /**
     * @return true if it is possible to know for sure if at EOF, and it is known for sure.
     * If the input stream is a ByteArrayInputStream, this is faster than causing a RuntimeEOFException
     * to be thrown.
     */
    public boolean knownAtEof() {
        if (isWriting) {
            throw new IllegalStateException("Calling knownAtEof method on BinaryCodec open for write.");
        }
        try {
            return inputStream instanceof ByteArrayInputStream && inputStream.available() == 0;
        } catch (IOException e) {
            throw new RuntimeIOException(constructErrorMessage("available() error"), e);
        }
    }

    /**
     * Read a string off the input stream, as ASCII bytes
     *
     * @param length length of string to read
     * @return String read from stream
     */
    public String readString(final int length) {
        final byte[] buffer;
        // Recycle single buffer if possible
        if (length <= scratchBuffer.length) {
            buffer = scratchBuffer;
        } else {
            buffer = new byte[length];

        }
        readBytes(buffer, 0, length);

        return StringUtil.bytesToString(buffer, 0, length);
    }

    /**
     * Read ASCII bytes from the input stream until a null byte is read
     * @return String constructed from the ASCII bytes read
     */
    public String readNullTerminatedString() {
        return StringUtil.readNullTerminatedString(this);
    }

    /**
     * Read an int length, and then a String of that length
     * @param devourNull if true, the length include a null terminator, which is read and discarded
     */
    public String readLengthAndString(final boolean devourNull) {
        int length = readInt();
        if (devourNull) {
            --length;
        }
        final String ret = readString(length);
        if (devourNull) {
            readByte();
        }
        return ret;
    }

    private void readByteBuffer(final int numBytes) {
        assert(numBytes <= byteBuffer.capacity());
        readBytes(byteBuffer.array(), 0, numBytes);
        byteBuffer.limit(byteBuffer.capacity());
        byteBuffer.position(numBytes);
    }

    /**
     * Read an int off the input stream
     *
     * @return int from input stream
     */
    public int readInt() {
        readByteBuffer(4);
        byteBuffer.flip();
        return byteBuffer.getInt();
    }

    /**
     * Reads a double off the input stream
     *
     * @return double
     */
    public double readDouble() {
        readByteBuffer(8);
        byteBuffer.flip();
        return byteBuffer.getDouble();
    }

    /**
     * Reads a long off the input stream
     *
     * @return long
     */
    public long readLong()  {
        readByteBuffer(8);
        byteBuffer.flip();
        return byteBuffer.getLong();
    }

    public short readShort() {
        readByteBuffer(2);
        byteBuffer.flip();
        return byteBuffer.getShort();
    }

    /**
     * Reads a float off the input stream
     *
     * @return float
     */
    public float readFloat() {
        readByteBuffer(4);
        byteBuffer.flip();
        return byteBuffer.getFloat();
    }

    /**
     * Reads a boolean off the input stream, represented as a byte with value 1 or 0
     *
     * @return boolean
     */
    public boolean readBoolean() {
        return (((int)readByte()) == 1);
    }

    /**
     * Reads an 8-bit unsigned byte from the input stream.
     * This method assumes little-endianness.
     */
    public short readUByte() {
        readByteBuffer(1);
        byteBuffer.put((byte)0);
        byteBuffer.flip();
        return byteBuffer.getShort();
    }

    /**
     * Reads a 16-bit unsigned short from the input stream.
     * This method assumes little-endianness.
     */
    public int readUShort() {
        readByteBuffer(2);
        byteBuffer.putShort((short)0);
        byteBuffer.flip();
        return byteBuffer.getInt();
    }

    /**
     * Reads a 32-bit unsigned int from the input stream.
     * This method assumes little-endianness.
     */
    public long readUInt() {
        readByteBuffer(4);
        byteBuffer.putInt(0);
        byteBuffer.flip();
        return byteBuffer.getLong();
    }

    /**
     * Close the appropriate stream
     */
    public void close() {
        try {
            if (this.isWriting) {
                // To the degree possible, make sure the bytes get forced to the file system,
                // or else cause an exception to be thrown.
                this.outputStream.flush();
                if (this.outputStream instanceof FileOutputStream) {
                    FileOutputStream fos = (FileOutputStream)this.outputStream;
                    try {
                        fos.getFD().sync();
                    } catch (SyncFailedException e) {
                        // Since the sync is belt-and-suspenders anyway, don't throw an exception if it fails,
                        // because on some OSs it will fail for some types of output.  E.g. writing to /dev/null
                        // on some Unixes.
                    }
                }
                this.outputStream.close();
            }
            else this.inputStream.close();
        } catch (IOException e) {
            throw new RuntimeIOException(e.getMessage(), e);
        }
    }

    private String constructErrorMessage(final String msg) {
        final StringBuilder sb = new StringBuilder(msg);
        sb.append("; BinaryCodec in ");
        sb.append(isWriting? "write": "read");
        sb.append("mode; ");
        final String filename = isWriting? outputFileName: inputFileName;
        if (filename != null) {
            sb.append("file: ");
            sb.append(filename);
        } else  {
            sb.append("streamed file (filename not available)");
        }
        return sb.toString();
    }

    //////////////////////////////////////////////////
    // Some getters                                 //
    //////////////////////////////////////////////////


    public String getInputFileName() {
        return inputFileName;
    }

    public String getOutputFileName() {
        return outputFileName;
    }

    public void setOutputFileName(final String outputFileName) {
        this.outputFileName = outputFileName;
    }

    public void setInputFileName(final String inputFileName) {
        this.inputFileName = inputFileName;
    }

    public boolean isWriting() {
        return isWriting;
    }

    public OutputStream getOutputStream() {
        return outputStream;
    }

    public InputStream getInputStream() {
        return inputStream;
    }

    public void setInputStream(final InputStream is) {
        isWriting = false;
        this.inputStream = is;
    }

    public void setOutputStream(final OutputStream os) {
        isWriting = true;
        this.outputStream = os;

    }
}
