info.bioinfweb.commons.collections.bitstorage

Interface BitField

public interface BitField

Interface that allows to read and write primitive data types from and to a field of bits. Implementing classes can be used to store huge amounts of data into the RAM without each element using more bits than necessary.

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
void	copyBits(long sourceStart, long numberOfBits, long destStart) Copies the specified number of bits from one position in the bit field to another.
void	insertBits(long start, long numberOfBits) Inserts the specified number of bits at the specified position of the bit field and moves all bits with indices >= start to the right.
long	length() Returns the current length of the bit field.
void	moveBits(long sourceStart, long numberOfBits, long destStart) Moves the specified number of bits from one position in the bit field to another.
boolean	readBoolean(long position) Interprets the bit at the specified position as a boolean value.
byte	readByte(long start, long numberOfBits) Reads a signed integer with the specified length and returns it as a byte value.
int	readInt(long start, long numberOfBits) Reads a signed integer with the specified length and returns it as a int value.
long	readLong(long start, long numberOfBits) Reads a signed integer with the specified length and returns it as a long value.
short	readShort(long start, long numberOfBits) Reads a signed integer with the specified length and returns it as a short value.
byte	readUnsignedByte(long start, long numberOfBits) Reads an unsigned integer with the specified length and returns it as a byte value.
int	readUnsignedInt(long start, long numberOfBits) Reads an unsigned integer with the specified length and returns it as a int value.
long	readUnsignedLong(long start, long numberOfBits) Reads an unsigned integer with the specified length and returns it as a long value.
short	readUnsignedShort(long start, long numberOfBits) Reads an unsigned integer with the specified length and returns it as a short value.
void	removeBits(long start, long numberOfBits) Removes the specified number of bits from the specified position of the bit field and moves all bits with indices >= start + numberOfBits to the left.
void	writeBoolean(boolean value, long position) Sets the bit at the specified position according the specified boolean value.
void	writeByte(byte value, long start, long numberOfBits)
void	writeInt(int value, long start, long numberOfBits)
void	writeLong(long value, long start, long numberOfBits)
void	writeShort(short value, long start, long numberOfBits)
void	writeUnsignedByte(byte value, long start, long numberOfBits)
void	writeUnsignedInt(int value, long start, long numberOfBits)
void	writeUnsignedLong(long value, long start, long numberOfBits)
void	writeUnsignedShort(short value, long start, long numberOfBits)

Method Detail

insertBits

void insertBits(long start,
                long numberOfBits)
         throws BitIndexOutOfBoundException

Inserts the specified number of bits at the specified position of the bit field and moves all bits with indices >= start to the right. The new bit area is not necessarily initialized.

Parameters:

start - the index where the first bit shall be inserted

numberOfBits - the number of bits to be inserted

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

removeBits

void removeBits(long start,
                long numberOfBits)
         throws BitIndexOutOfBoundException

Removes the specified number of bits from the specified position of the bit field and moves all bits with indices >= start + numberOfBits to the left.

Parameters:

start - the index where the first bit shall be inserted

numberOfBits - the number of bits to be inserted

Throws:

BitIndexOutOfBoundException

copyBits

void copyBits(long sourceStart,
              long numberOfBits,
              long destStart)
       throws BitIndexOutOfBoundException

Copies the specified number of bits from one position in the bit field to another.

Parameters:

sourceStart - the index of the first bit to be copied

numberOfBits - the number of bits to be copied

destStart - the index where the left most bit of the copied area shall be written to

Throws:

BitIndexOutOfBoundException - if sourceStart or sourceStart are lower than 0 or sourceStart + numberOfBits or sourceStart + numberOfBits are greater than length() or if the source and the destination area overlap

moveBits

void moveBits(long sourceStart,
              long numberOfBits,
              long destStart)
       throws BitIndexOutOfBoundException

Moves the specified number of bits from one position in the bit field to another. This method acts similar to copyBits(long, long, long) with the only difference that the source and the destination area are allowed to overlap.

Parameters:

sourceStart - the index of the first bit to be copied

numberOfBits - the number of bits to be copied

destStart - the index where the left most bit of the moved area shall be written to

Throws:

BitIndexOutOfBoundException - if sourceStart or sourceStart are lower than 0 or sourceStart + numberOfBits or sourceStart + numberOfBits are greater than length()

length

long length()

Returns the current length of the bit field.

Returns:

the length of the field in bits

readByte

byte readByte(long start,
              long numberOfBits)
       throws BitIndexOutOfBoundException

Reads a signed integer with the specified length and returns it as a byte value.

Parameters:

start - the index of the bit in the bit field that shall be interpreted as the beginning of the integer value

numberOfBits - the number of bits to be read (The first left most bit determines the algebraic sign.)

Returns:

the read bits interpreted as an signed integer

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

readUnsignedByte

byte readUnsignedByte(long start,
                      long numberOfBits)
               throws BitIndexOutOfBoundException

Reads an unsigned integer with the specified length and returns it as a byte value.

Parameters:

start - the index of the bit in the bit field that shall be interpreted as the beginning of the integer value

numberOfBits - the number of bits to be read

Returns:

the read bits interpreted as an unsigned integer

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

writeByte

void writeByte(byte value,
               long start,
               long numberOfBits)
        throws BitIndexOutOfBoundException

Parameters:

value -

start -

numberOfBits -

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

writeUnsignedByte

void writeUnsignedByte(byte value,
                       long start,
                       long numberOfBits)
                throws BitIndexOutOfBoundException

Throws:

BitIndexOutOfBoundException

readShort

short readShort(long start,
                long numberOfBits)
         throws BitIndexOutOfBoundException

Reads a signed integer with the specified length and returns it as a short value.

Parameters:

start - the index of the bit in the bit field that shall be interpreted as the beginning of the integer value

numberOfBits - the number of bits to be read (The first left most bit determines the algebraic sign.)

Returns:

the read bits interpreted as an signed integer

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

readUnsignedShort

short readUnsignedShort(long start,
                        long numberOfBits)
                 throws BitIndexOutOfBoundException

Reads an unsigned integer with the specified length and returns it as a short value.

Parameters:

start - the index of the bit in the bit field that shall be interpreted as the beginning of the integer value

numberOfBits - the number of bits to be read

Returns:

the read bits interpreted as an unsigned integer

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

writeShort

void writeShort(short value,
                long start,
                long numberOfBits)
         throws BitIndexOutOfBoundException

Throws:

BitIndexOutOfBoundException

writeUnsignedShort

void writeUnsignedShort(short value,
                        long start,
                        long numberOfBits)
                 throws BitIndexOutOfBoundException

Throws:

BitIndexOutOfBoundException

readInt

int readInt(long start,
            long numberOfBits)
     throws BitIndexOutOfBoundException

Reads a signed integer with the specified length and returns it as a int value.

Parameters:

start - the index of the bit in the bit field that shall be interpreted as the beginning of the integer value

numberOfBits - the number of bits to be read (The first left most bit determines the algebraic sign.)

Returns:

the read bits interpreted as an signed integer

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

readUnsignedInt

int readUnsignedInt(long start,
                    long numberOfBits)
             throws BitIndexOutOfBoundException

Reads an unsigned integer with the specified length and returns it as a int value.

Parameters:

start - the index of the bit in the bit field that shall be interpreted as the beginning of the integer value

numberOfBits - the number of bits to be read

Returns:

the read bits interpreted as an unsigned integer

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

writeInt

void writeInt(int value,
              long start,
              long numberOfBits)
       throws BitIndexOutOfBoundException

Throws:

BitIndexOutOfBoundException

writeUnsignedInt

void writeUnsignedInt(int value,
                      long start,
                      long numberOfBits)
               throws BitIndexOutOfBoundException

Throws:

BitIndexOutOfBoundException

readLong

long readLong(long start,
              long numberOfBits)
       throws BitIndexOutOfBoundException

Reads a signed integer with the specified length and returns it as a long value.

Parameters:

start - the index of the bit in the bit field that shall be interpreted as the beginning of the integer value

numberOfBits - the number of bits to be read (The first left most bit determines the algebraic sign.)

Returns:

the read bits interpreted as an signed integer

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

readUnsignedLong

long readUnsignedLong(long start,
                      long numberOfBits)
               throws BitIndexOutOfBoundException

Reads an unsigned integer with the specified length and returns it as a long value.

Parameters:

start - the index of the bit in the bit field that shall be interpreted as the beginning of the integer value

numberOfBits - the number of bits to be read

Returns:

the read bits interpreted as an unsigned integer

Throws:

BitIndexOutOfBoundException - if start is lower than 0 or start + numberOfBits is greater than length()

writeLong

void writeLong(long value,
               long start,
               long numberOfBits)
        throws BitIndexOutOfBoundException

Throws:

BitIndexOutOfBoundException

writeUnsignedLong

void writeUnsignedLong(long value,
                       long start,
                       long numberOfBits)
                throws BitIndexOutOfBoundException

Throws:

BitIndexOutOfBoundException

readBoolean

boolean readBoolean(long position)
             throws BitIndexOutOfBoundException

Interprets the bit at the specified position as a boolean value.

Parameters:

position - the position of the bit to be read

Returns:

true if the specified bit is set, false otherwise

Throws:

BitIndexOutOfBoundException - if position is lower than 0 or greater or equal to length()

writeBoolean

void writeBoolean(boolean value,
                  long position)
           throws BitIndexOutOfBoundException

Sets the bit at the specified position according the specified boolean value.

Parameters:

value - Determine whether the bit shall be set to 0 or 1

position - the index of the bit in the field

Throws:

BitIndexOutOfBoundException - if position is lower than 0 or greater or equal to length()