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/*
* 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;
import java.nio.file.Files;
import java.nio.file.Path;
/**
* 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};
public static final long MAX_UBYTE = (Byte.MAX_VALUE * 2) + 1;
public static final long MAX_USHORT = (Short.MAX_VALUE * 2) + 1;
public 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 its mode to writing or not
*
* @param path file to be written to or read from
* @param writing whether the file is being written to
*/
public BinaryCodec(final Path path, final boolean writing) {
this();
try {
this.isWriting = writing;
if (this.isWriting) {
this.outputStream = IOUtil.maybeBufferOutputStream(Files.newOutputStream(path));
this.outputFileName = path.getFileName().toString();
} else {
this.inputStream = IOUtil.maybeBufferInputStream(Files.newInputStream(path));
this.inputFileName = path.getFileName().toString();
}
} catch (FileNotFoundException e) {
throw new RuntimeIOException("File not found: " + path, e);
} catch (IOException e) {
throw new RuntimeIOException("Error opening: " + path, e);
}
}
/**
* Constructs BinaryCodec from a file and set its 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(IOUtil.toPath(file), writing);
}
/**
* Constructs BinaryCodec from a file name and set its 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 {
// Some implementations of InputStream do not behave well when the buffer is empty and length is zero, for
// example ByteArrayInputStream, so we must check for length equal to zero.
// See: https://bugs.java.com/view_bug.do?bug_id=6766844
return (length == 0) ? 0 : 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
*/
@Override
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 ")
.append(isWriting? "write": "read").append("mode; ");
final String filename = isWriting? outputFileName: inputFileName;
if (filename != null) {
sb.append("file: ").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;
}
}
