org.terrier.compression.bit

Class BitFile

java.lang.Object

org.terrier.compression.bit.BitFile

All Implemented Interfaces:

Closeable, AutoCloseable, BitIn, BitInSeekable, BitOut

Deprecated.

Use BitFileBuffered and BitOutputStream instead

public class BitFile
extends Object
implements BitInSeekable, BitIn, BitOut

This class encapsulates a random access file and provides the functionalities to read and write binary encoded, unary encoded and gamma encoded integers greater than zero, as well as specifying their offset in the file. It is employed by the DirectFile and the InvertedFile classes. Use the getBit/ByteOffset methods only for writting, and not for reading. This class contains the methods in both BitInputStream and BitOutputStream. The numbers are written into a byte starting from the most significant bit (i.e, left to right). The sequence of method calls to write a sequence of gamma encoded and unary encoded numbers is:

  file.writeReset();
  long startByte1 = file.getByteOffset();
  byte startBit1 = file.getBitOffset();
  file.writeGamma(20000);
  file.writeUnary(2);
  file.writeGamma(35000);
  file.writeUnary(1);
  file.writeGamma(3);
  file.writeUnary(2);
  long endByte1 = file.getByteOffset();
  byte endBit1 = file.getBitOffset();
  if (endBit1 == 0 && endByte1 > 0) {
      endBit1 = 7;
      endByte1--;
  }
 

while for reading a sequence of numbers the sequence of calls is:

  file.readReset(startByte1, startBit1, endByte1, endBit1);
  int gamma = file.readGamma();
  int unary = file.readUnary();
 

Author:

Roi Blanco

Field Summary

Fields

Modifier and Type	Field and Description
protected int	bitOffset Deprecated. The bit offset.
protected byte[]	buffer Deprecated. Write buffer
protected int	bufferPointer Deprecated. Pointer for the buffer
protected int	bufferSize Deprecated. Size of the buffer (it has to be 4 * k)
protected long	byteOffset Deprecated. The byte offset.
protected int	byteToWrite Deprecated. A int to write to the stream.
protected static String	DEFAULT_FILE_MODE Deprecated. Default file mode access for a BitFile object.
protected static int	DEFAULT_SIZE Deprecated. Default size
protected RandomDataInput	file Deprecated. The underlying file
protected byte[]	inBuffer Deprecated. Buffer for reads
protected boolean	isWriteMode Deprecated. Indicates if we are writting or reading
protected static org.apache.log4j.Logger	logger Deprecated. The logger used
protected int	readBits Deprecated. Number of bits read so far
protected int	readByteOffset Deprecated. The current byte offset to be read
protected RandomDataOutput	writeFile Deprecated. Same object as file, but cast to RandomDataOutput

Fields inherited from interface org.terrier.compression.bit.BitIn

USUAL_EXTENSION

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	BitFile() Deprecated. do nothing constructor
	BitFile(File _file) Deprecated. Constructs an instance of the class for a given filename, "rw" permissions
	BitFile(File _file, String access) Deprecated. Constructs an instance of the class for a given file and an acces method to the file
	BitFile(RandomDataInput data) Deprecated. Constructs an instance of the class for a given RandomDataInput instance accessing a bit compressed file/stream
	BitFile(String filename) Deprecated. Constructs an instance of the class for a given filename, "rw" permissions
	BitFile(String filename, String access) Deprecated. Constructs an instance of the class for a given filename and an acces method to the file

Method Summary

Methods

Modifier and Type	Method and Description
void	align() Deprecated. Aligns the stream to the next byte
void	close() Deprecated. Closes the file.
byte	getBitOffset() Deprecated. Returns the bit offset in the last byte.
long	getByteOffset() Deprecated. Returns the byte offset of the stream.
protected void	init() Deprecated. Initialises the variables, used internally
int	readBinary(int len) Deprecated. Reads a binary integer from the already read buffer.
int	readDelta() Deprecated. Reads a delta encoded integer from the underlying stream
int	readGamma() Deprecated. Reads a gamma encoded integer from the underlying stream
int	readGolomb(int b) Deprecated. Reads a Golomb encoded integer
protected void	readIn() Deprecated. Reads a new byte from the InputStream if we have finished with the current one.
void	readInterpolativeCoding(int[] data, int offset, int len, int lo, int hi) Deprecated. Reads a sequence of numbers from the stream interpolative coded.
int	readMinimalBinary(int b) Deprecated. Reads a binary encoded integer, given an upper bound
int	readMinimalBinaryZero(int b) Deprecated. Reads a minimal binary encoded number, when the upper bound can b zero.
BitIn	readReset(long startByteOffset, byte startBitOffset) Deprecated. Reads from the file a specific number of bytes and after this call, a sequence of read calls may follow.
BitIn	readReset(long startByteOffset, byte startBitOffset, long endByteOffset, byte endBitOffset) Deprecated. Reads from the file a specific number of bytes and after this call, a sequence of read calls may follow.
int	readSkewedGolomb(int b) Deprecated. Reads a skewed-golomb encoded integer from the underlying stream Consider a bucket-vector v = <0, 2b, 4b, ...
int	readUnary() Deprecated. Reads a unary encoded integer from the underlying stream
void	skipBits(int len) Deprecated. Skip a number of bits in the current input stream
void	skipBytes(long len) Deprecated. Skip a number of bytes while reading the bit file.
int	writeBinary(int len, int x) Deprecated. Writes an integer in binary format to the stream.
int	writeDelta(int x) Deprecated. Writes an integer x into the stream using delta encoding.
void	writeFlush() Deprecated. Flushes the OuputStream (empty method)
int	writeGamma(int x) Deprecated. Writes an integer x into the stream using gamma encoding.
int	writeGolomb(int x, int b) Deprecated. Writes and integer x into the stream using golomb coding.
protected int	writeInCurrent(int b, int len) Deprecated. Writes a number in the current byte we are using.
int	writeInt(int x, int len) Deprecated. Writes an integer x into the underlying OutputStream.
protected void	writeIntBuffer(int writeMe) Deprecated. Flushes the int currently being written into the buffer, and if it is necessary, it flush the buffer to the underlying OutputStream
protected void	writeIntBufferToBit(int writeMe, int _bitOffset) Deprecated. Writes the current integer used into the buffer, taking into account the number of bits written.
int	writeInterpolativeCode(int[] data, int offset, int len, int lo, int hi) Deprecated. Writes a sequence of integers using interpolative coding.
int	writeMinimalBinary(int x, int b) Deprecated. Writes an integer x using minimal binary encoding, given an upper bound.
void	writeReset() Deprecated. Set the write mode to true
int	writeSkewedGolomb(int x, int b) Deprecated. Writes and integer x into the stream using skewed-golomb coding.
int	writeUnary(int x) Deprecated. Writes an integer x using unary encoding.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Deprecated.

The logger used

buffer

protected byte[] buffer

Deprecated.

Write buffer

bufferPointer

protected int bufferPointer

Deprecated.

Pointer for the buffer

bufferSize

protected int bufferSize

Deprecated.

Size of the buffer (it has to be 4 * k)

DEFAULT_SIZE

protected static final int DEFAULT_SIZE

Deprecated.

Default size

See Also:

Constant Field Values

DEFAULT_FILE_MODE

protected static final String DEFAULT_FILE_MODE

Deprecated.

Default file mode access for a BitFile object. Currently "rw".

See Also:

Constant Field Values

byteOffset

protected long byteOffset

Deprecated.

The byte offset.

readByteOffset

protected int readByteOffset

Deprecated.

The current byte offset to be read

bitOffset

protected int bitOffset

Deprecated.

The bit offset.

byteToWrite

protected int byteToWrite

Deprecated.

A int to write to the stream.

isWriteMode

protected boolean isWriteMode

Deprecated.

Indicates if we are writting or reading

file

protected RandomDataInput file

Deprecated.

The underlying file

writeFile

protected RandomDataOutput writeFile

Deprecated.

Same object as file, but cast to RandomDataOutput

inBuffer

protected byte[] inBuffer

Deprecated.

Buffer for reads

readBits

protected int readBits

Deprecated.

Number of bits read so far

Constructor Detail

BitFile

public BitFile(RandomDataInput data)

Deprecated.

Constructs an instance of the class for a given RandomDataInput instance accessing a bit compressed file/stream

Parameters:

data - a RandomDataInput instance containing the bit compressed data

BitFile

public BitFile(File _file,
       String access)

Deprecated.

Constructs an instance of the class for a given file and an acces method to the file

Parameters:

_file - File to read/write

access - String indicating the access permissions of the file

BitFile

public BitFile(String filename,
       String access)

Deprecated.

Constructs an instance of the class for a given filename and an acces method to the file

Parameters:

filename - java.lang.String the name of the underlying file

access - String indicating the access permissions of the file

BitFile

public BitFile(String filename)

Deprecated.

Constructs an instance of the class for a given filename, "rw" permissions

Parameters:

filename - java.lang.String the name of the underlying file

BitFile

public BitFile(File _file)

Deprecated.

Constructs an instance of the class for a given filename, "rw" permissions

Parameters:

_file - java.io.File

BitFile

protected BitFile()

Deprecated.

do nothing constructor

Method Detail

init

protected void init()

Deprecated.

Initialises the variables, used internally

getByteOffset

public long getByteOffset()

Deprecated.

Returns the byte offset of the stream. It corresponds to the position of the byte in which the next bit will be written. Use only when writting

Specified by:

getByteOffset in interface BitIn

Specified by:

getByteOffset in interface BitOut

Returns:

the byte offset in the stream.

getBitOffset

public byte getBitOffset()

Deprecated.

Returns the bit offset in the last byte. It corresponds to the position in which the next bit will be written. Use only when writting.

Specified by:

getBitOffset in interface BitIn

Specified by:

getBitOffset in interface BitOut

Returns:

the bit offset in the stream.

writeIntBuffer

protected void writeIntBuffer(int writeMe)
                       throws IOException

Deprecated.

Flushes the int currently being written into the buffer, and if it is necessary, it flush the buffer to the underlying OutputStream

Parameters:

writeMe - int to be written into the buffer

Throws:

IOException - if an I/O error occurs

writeInCurrent

protected int writeInCurrent(int b,
                 int len)
                      throws IOException

Deprecated.

Writes a number in the current byte we are using.

Parameters:

b - the number to write

len - the length of the number in bits

Returns:

the number of bits written

Throws:

IOException - if an I/O error occurs.

writeUnary

public int writeUnary(int x)
               throws IOException

Deprecated.

Writes an integer x using unary encoding. The encoding is a sequence of x -1 zeros and 1 one: 1, 01, 001, 0001, etc .. This method is not failsafe, it doesn't check if the argument is 0 or negative.

Specified by:

writeUnary in interface BitOut

Parameters:

x - the number to write

Returns:

the number of bits written

Throws:

IOException - if an I/O error occurs.

writeDelta

public int writeDelta(int x)
               throws IOException

Deprecated.

Writes an integer x into the stream using delta encoding. This method is not failsafe, it doesn't check if the argument is 0 or negative.

Specified by:

writeDelta in interface BitOut

Parameters:

x - the int number to write

Returns:

the number of bits written

Throws:

IOException - if an I/O error occurs.

writeGamma

public int writeGamma(int x)
               throws IOException

Deprecated.

Writes an integer x into the stream using gamma encoding. This method is not failsafe, it doesn't check if the argument is 0 or negative.

Specified by:

writeGamma in interface BitOut

Parameters:

x - the int number to write

Returns:

the number of bits written

Throws:

IOException - if an I/O error occurs.

writeInt

public int writeInt(int x,
           int len)
             throws IOException

Deprecated.

Writes an integer x into the underlying OutputStream. First, it checks if it fits into the current byte we are using for writing, and then it writes as many bytes as necessary

Specified by:

writeInt in interface BitOut

Parameters:

x - the int to write

len - length of the int in bits

Returns:

the number of bits written

Throws:

IOException - if an I/O error occurs.

writeFlush

public void writeFlush()

Deprecated.

Flushes the OuputStream (empty method)

readReset

public BitIn readReset(long startByteOffset,
              byte startBitOffset,
              long endByteOffset,
              byte endBitOffset)

Deprecated.

Reads from the file a specific number of bytes and after this call, a sequence of read calls may follow. The offsets given as arguments are inclusive. For example, if we call this method with arguments 0, 2, 1, 7, it will read in a buffer the contents of the underlying file from the third bit of the first byte to the last bit of the second byte.

Specified by:

readReset in interface BitInSeekable

Parameters:

startByteOffset - the starting byte to read from

startBitOffset - the bit offset in the starting byte

endByteOffset - the ending byte

endBitOffset - the bit offset in the ending byte. This bit is the last bit of this entry.

Returns:

Returns the BitIn object to use to read that data

readReset

public BitIn readReset(long startByteOffset,
              byte startBitOffset)
                throws IOException

Deprecated.

Reads from the file a specific number of bytes and after this call, a sequence of read calls may follow. The offsets given as arguments are inclusive. For example, if we call this method with arguments 0, 2, 1, 7, it will read in a buffer the contents of the underlying file from the third bit of the first byte to the last bit of the second byte.

Specified by:

readReset in interface BitInSeekable

Parameters:

startByteOffset - the starting byte to read from

startBitOffset - the bit offset in the starting byte

Returns:

Returns the BitIn object to use to read that data

Throws:

IOException

readGamma

public int readGamma()

Deprecated.

Reads a gamma encoded integer from the underlying stream

Specified by:

readGamma in interface BitIn

Returns:

the number read

readUnary

public int readUnary()

Deprecated.

Reads a unary encoded integer from the underlying stream

Specified by:

readUnary in interface BitIn

Returns:

the number read

readDelta

public int readDelta()
              throws IOException

Deprecated.

Reads a delta encoded integer from the underlying stream

Specified by:

readDelta in interface BitIn

Returns:

the number read

Throws:

IOException - if an I/O error occurs

readIn

protected void readIn()

Deprecated.

Reads a new byte from the InputStream if we have finished with the current one.

Throws:

IOException - if we have reached the end of the file

align

public void align()

Deprecated.

Aligns the stream to the next byte

Specified by:

align in interface BitIn

readBinary

public int readBinary(int len)

Deprecated.

Reads a binary integer from the already read buffer.

Specified by:

readBinary in interface BitIn

Parameters:

len - is the number of binary bits to read

Returns:

the decoded integer

skipBits

public void skipBits(int len)

Deprecated.

Skip a number of bits in the current input stream

Specified by:

skipBits in interface BitIn

Parameters:

len - The number of bits to skip

skipBytes

public void skipBytes(long len)
               throws IOException

Deprecated.

Skip a number of bytes while reading the bit file. After this opteration, getBitOffset() == 0, so use skipBits(int) to get getBitOffset() to desired value.

Specified by:

skipBytes in interface BitIn

Parameters:

len - The number of bytes to skip

Throws:

IOException - if an I/O error occurs

close

public void close()

Deprecated.

Closes the file. If the file has been written, it is also flushed to disk.

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

writeIntBufferToBit

protected void writeIntBufferToBit(int writeMe,
                       int _bitOffset)

Deprecated.

Writes the current integer used into the buffer, taking into account the number of bits written. Used when closing the file, to avoid unecessary byte writes. in that integer so far.

Parameters:

writeMe - int to write

_bitOffset - number of bits written so far in the int

writeReset

public void writeReset()
                throws IOException

Deprecated.

Set the write mode to true

Throws:

IOException

writeBinary

public int writeBinary(int len,
              int x)
                throws IOException

Deprecated.

Writes an integer in binary format to the stream.

Specified by:

writeBinary in interface BitOut

Parameters:

len - size in bits of the number.

x - the integer to write.

Returns:

the number of bits written.

Throws:

IOException - if an I/O error occurs.

writeMinimalBinary

public int writeMinimalBinary(int x,
                     int b)
                       throws IOException

Deprecated.

Writes an integer x using minimal binary encoding, given an upper bound. This method is not failsafe, it doesn't check if the argument is 0 or negative.

Specified by:

writeMinimalBinary in interface BitOut

Parameters:

x - the number to write

b - and strict bound for x

Returns:

the number of bits written

Throws:

IOException - if an I/O error occurs.

readMinimalBinary

public int readMinimalBinary(int b)
                      throws IOException

Deprecated.

Reads a binary encoded integer, given an upper bound

Specified by:

readMinimalBinary in interface BitIn

Parameters:

b - the upper bound

Returns:

the int read

Throws:

IOException - if an I/O error occurs

writeGolomb

public int writeGolomb(int x,
              int b)
                throws IOException

Deprecated.

Writes and integer x into the stream using golomb coding. This method is not failsafe, it doesn't check if the argument or the modulus is 0 or negative.

Specified by:

writeGolomb in interface BitOut

Parameters:

x - the number to write

b - the parameter for golomb coding

Returns:

the number of bits written

Throws:

IOException - if and I/O error occurs

readGolomb

public int readGolomb(int b)
               throws IOException

Deprecated.

Reads a Golomb encoded integer

Specified by:

readGolomb in interface BitIn

Parameters:

b - the golomb modulus

Returns:

the int read

Throws:

IOException - if and I/O error occurs

writeSkewedGolomb

public int writeSkewedGolomb(int x,
                    int b)
                      throws IOException

Deprecated.

Writes and integer x into the stream using skewed-golomb coding. Consider a bucket-vector v = <b, 2b, 4b, ... , 2^i b, ...> an integer x is coded as unary(k+1) where k is the index sum(i=0)(k) v_i < x <= sum(i=0)(k+1)
, so k = log(x/b + 1) sum_i = b(2^n -1) (geometric progression) and the remainder with log(v_k) bits in binary if lower = ceil(x/b) -> lower = 2^i * b -> i = log(ceil(x/b)) + 1 the remainder x - sum_i 2^i*b - 1 = x - b(2^n - 1) - 1 is coded with floor(log(v_k)) bits This method is not failsafe, it doesn't check if the argument or the modulus is 0 or negative.

Specified by:

writeSkewedGolomb in interface BitOut

Parameters:

x - the number to write

b - the parameter for golomb coding

Returns:

the number of bits written

Throws:

IOException - if and I/O error occurs

writeInterpolativeCode

public int writeInterpolativeCode(int[] data,
                         int offset,
                         int len,
                         int lo,
                         int hi)
                           throws IOException

Deprecated.

Writes a sequence of integers using interpolative coding. The data must be sorted (increasing order).

Specified by:

writeInterpolativeCode in interface BitOut

Parameters:

data - the vector containing the integer sequence.

offset - the offset into data where the sequence starts.

len - the number of integers to code.

lo - a lower bound (must be smaller than or equal to the first integer in the sequence).

hi - an upper bound (must be greater than or equal to the last integer in the sequence).

Returns:

the number of written bits.

Throws:

IOException - if an I/O error occurs.

readSkewedGolomb

public int readSkewedGolomb(int b)
                     throws IOException

Deprecated.

Reads a skewed-golomb encoded integer from the underlying stream Consider a bucket-vector v = <0, 2b, 4b, ... , 2^i b, ...> The sum of the elements in the vector goes b, 3b, 7b, 2^(i-1)*b

Specified by:

readSkewedGolomb in interface BitIn

Returns:

the number read

Throws:

IOException - if an I/O error occurs

readInterpolativeCoding

public void readInterpolativeCoding(int[] data,
                           int offset,
                           int len,
                           int lo,
                           int hi)
                             throws IOException

Deprecated.

Reads a sequence of numbers from the stream interpolative coded.

Specified by:

readInterpolativeCoding in interface BitIn

Parameters:

data - the result vector

offset - offset where to write in the vector

len - the number of integers to decode.

lo - a lower bound (the same one passed to writeInterpolativeCoding)

hi - an upper bound (the same one passed to writeInterpolativeCoding)

Throws:

IOException - if an I/O error occurs

readMinimalBinaryZero

public int readMinimalBinaryZero(int b)
                          throws IOException

Deprecated.

Reads a minimal binary encoded number, when the upper bound can b zero. Used to interpolative code

Specified by:

readMinimalBinaryZero in interface BitIn

Parameters:

b - the upper bound

Returns:

the int read

Throws:

IOException - if an I/O error occurs