Package ubic.basecode.dataStructure.matrix

Class CompressedBitMatrix<R,C>

java.lang.Object

ubic.basecode.dataStructure.matrix.AbstractMatrix<R,C,double[]>

ubic.basecode.dataStructure.matrix.CompressedBitMatrix<R,C>

All Implemented Interfaces:

Serializable, Matrix2D<R,C,double[]>, ObjectMatrix<R,C,double[]>

public class CompressedBitMatrix<R,C>
extends AbstractMatrix<R,C,double[]>
implements ObjectMatrix<R,C,double[]>

Named compressed sparse bit matrix.

Author:

xwan

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static long	BIT1
static int	BITS_PER_ELEMENT

Fields inherited from class ubic.basecode.dataStructure.matrix.AbstractMatrix

MAX_ROWS_TO_PRINT

Constructor Summary

Constructors

Constructor	Description
CompressedBitMatrix(int rows, int cols, int totalBitsPerItem)	Constructs a matrix with specified rows, columns, and total bits per cell

Method Summary

Modifier and Type	Method	Description
int	bitCount(int r, int c)	Count the number of one-bits at the specified cell position
int	columns()	Get the number of columns the matrix has.
double[]	get(int row, int col)
boolean	get(int row, int col, int index)	Checks the bit of the specified cell at the specified index.
long[]	getAllBits(int row, int col)	Returns all of the bits for a cell
int	getBitNum()	Returns the total number of bits in a matrix cell
double[]	getByKeys(R r, C c)
double[][]	getColumn(int i)
double[]	getEntry(int row, int column)
double[][]	getRow(int i)
int[]	getRowBitCount(int row)
boolean	isMissing(int i, int j)	Check if the value at a given index is missing.
int	overlap(int row1, int col1, int row2, int col2)	Counts the number of one-bits that are in common between the two specified cells; i.e. performs an AND operation on the two bit vectors and counts the remaining 1 bits.
void	reset(int r, int c)
int	rows()	Get the number of rows the matrix has
void	set(int row, int col, double[] val)	Set the matrix cell to the specified bit vector
void	set(int row, int col, int index)	Sets the bit of the specified cell at the specified index to 1.
void	setByKeys(R r, C c, double[] v)
int	size()
ObjectMatrix<R,C,double[]>	subset(int startRow, int startCol, int numRow, int numCol)
ObjectMatrix<R,C,double[]>	subsetColumns(List<C> columns)
void	toFile(String fileName)	Save the matrix to the specified file
long	totalBitCount()	Number of ones in the entire matrix.
void	unset(int row, int col, int index)

Methods inherited from class ubic.basecode.dataStructure.matrix.AbstractMatrix

addColumnName, addRowName, asDoubles, assign, checkColRange, checkRowRange, containsColumnName, containsRowName, getColIndexByName, getColName, getColNames, getRowIndexByName, getRowName, getRowNameMapIterator, getRowNames, hasColNames, hasMissingValues, hasRow, hasRowNames, numMissing, setColumnName, setColumnNames, setRowName, setRowNames

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.basecode.dataStructure.matrix.Matrix2D

addColumnName, asDoubles, assign, containsColumnName, containsRowName, getColIndexByName, getColName, getColNames, getRowIndexByName, getRowName, getRowNameMapIterator, getRowNames, hasColNames, hasRow, hasRowNames, numMissing, setColumnName, setColumnNames, setRowName, setRowNames

Field Details

BIT1

public static long BIT1

BITS_PER_ELEMENT

public static int BITS_PER_ELEMENT

Constructor Details

CompressedBitMatrix

public CompressedBitMatrix(int rows,
 int cols,
 int totalBitsPerItem)

Constructs a matrix with specified rows, columns, and total bits per cell

Implementation note: this is created by maintaining one or more Double matrices; the Doubles are used as bit fields.

Parameters:

rows - - number of rows in the matrix

cols - - number of columns in the matrix

totalBitsPerItem - - the number of bits for each cell

Method Details

bitCount

public int bitCount(int r,
 int c)

Count the number of one-bits at the specified cell position

Parameters:

r -

c -

Returns:

columns

public int columns()

Description copied from interface: Matrix2D

Get the number of columns the matrix has.

Specified by:

columns in interface Matrix2D<R,C,double[]>

Returns:

int

get

public double[] get(int row,
 int col)

Specified by:

get in interface ObjectMatrix<R,C,double[]>

get

public boolean get(int row,
 int col,
 int index)

Checks the bit of the specified cell at the specified index.

Parameters:

row - - matrix row

col - - matrix column

index - - bit vector index

Returns:

true if bit is 1, false if 0.

getAllBits

public long[] getAllBits(int row,
 int col)

Returns all of the bits for a cell

Parameters:

row - - the cell row

col - - the cell column

Returns:

all the bits encoded as an array of longs

getBitNum

public int getBitNum()

Returns the total number of bits in a matrix cell

Returns:

the number of bits per cell

getByKeys

public double[] getByKeys(R r,
 C c)

Specified by:

getByKeys in interface Matrix2D<R,C,double[]>

Parameters:

r -

c -

getColumn

public double[][] getColumn(int i)

Specified by:

getColumn in interface ObjectMatrix<R,C,double[]>

getEntry

public double[] getEntry(int row,
 int column)

Specified by:

getEntry in interface Matrix2D<R,C,double[]>

Parameters:

row -

column -

Returns:

getRow

public double[][] getRow(int i)

Specified by:

getRow in interface ObjectMatrix<R,C,double[]>

getRowBitCount

public int[] getRowBitCount(int row)

Parameters:

row -

Returns:

- array of counts of one-bits for each cell in the row.

isMissing

public boolean isMissing(int i,
 int j)

Description copied from interface: Matrix2D

Check if the value at a given index is missing.

Specified by:

isMissing in interface Matrix2D<R,C,double[]>

Parameters:

i - row

j - column

Returns:

true if the value is missing, false otherwise.

overlap

public int overlap(int row1,
 int col1,
 int row2,
 int col2)

Counts the number of one-bits that are in common between the two specified cells; i.e. performs an AND operation on the two bit vectors and counts the remaining 1 bits.

Parameters:

row1 - - cell 1 row

col1 - - cell 1 column

row2 - - cell 2 row

col2 - - cell 2 column

Returns:

number of bits in common

reset

public void reset(int r,
 int c)

rows

public int rows()

Description copied from interface: Matrix2D

Get the number of rows the matrix has

Specified by:

rows in interface Matrix2D<R,C,double[]>

Returns:

int

set

public void set(int row,
 int col,
 double[] val)

Set the matrix cell to the specified bit vector

Specified by:

set in interface Matrix2D<R,C,double[]>

Parameters:

row -

col -

val -

set

public void set(int row,
 int col,
 int index)

Sets the bit of the specified cell at the specified index to 1.

Parameters:

row - - matrix row

col - - matrix column

index - - bit vector index

setByKeys

public void setByKeys(R r,
 C c,
 double[] v)

Specified by:

setByKeys in interface Matrix2D<R,C,double[]>

Parameters:

r -

c -

v -

size

public int size()

Specified by:

size in class AbstractMatrix<R,C,double[]>

subset

public ObjectMatrix<R,C,double[]> subset(int startRow,
 int startCol,
 int numRow,
 int numCol)

Specified by:

subset in interface ObjectMatrix<R,C,double[]>

Parameters:

startRow -

startCol -

numRow -

numCol -

Returns:

subsetColumns

public ObjectMatrix<R,C,double[]> subsetColumns(List<C> columns)

Specified by:

subsetColumns in interface ObjectMatrix<R,C,double[]>

Parameters:

columns -

Returns:

toFile

public void toFile(String fileName)
            throws IOException

Save the matrix to the specified file

Parameters:

fileName - - save file

Throws:

IOException

totalBitCount

public long totalBitCount()

Number of ones in the entire matrix.

Returns:

unset

public void unset(int row,
 int col,
 int index)