org.biojava.nbio.structure.math

Class SparseSquareMatrix

java.lang.Object

org.biojava.nbio.structure.math.SparseSquareMatrix

All Implemented Interfaces:

Serializable

public class SparseSquareMatrix
extends Object
implements Serializable

A sparse, square matrix, implementing using two arrays of sparse vectors, one representation for the rows and one for the columns. For matrix-matrix product, we might also want to store the column representation. Derived from http://introcs.cs.princeton.edu/java/44st/SparseMatrix.java.html For additional documentation, see Section 4.4 of Introduction to Programming in Java: An Interdisciplinary Approach by Robert Sedgewick and Kevin Wayne.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
SparseSquareMatrix(int N) initialize an N-by-N matrix of all 0s

Method Summary

Modifier and Type	Method and Description
double	get(int i, int j) access a value at i,j
int	nnz() return the number of nonzero entries (not the most efficient implementation)
SparseSquareMatrix	plus(SparseSquareMatrix B) return C = A + B
void	put(int i, int j, double value) set A[i][j] = value
SparseVector	times(SparseVector x)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SparseSquareMatrix

public SparseSquareMatrix(int N)

initialize an N-by-N matrix of all 0s

Parameters:

N - - size

Method Detail

put

public void put(int i,
                int j,
                double value)

set A[i][j] = value

Parameters:

i -

j -

value -

get

public double get(int i,
                  int j)

access a value at i,j

Parameters:

i -

j -

Returns:

return A[i][j]

nnz

public int nnz()

return the number of nonzero entries (not the most efficient implementation)

Returns:

times

public SparseVector times(SparseVector x)

Parameters:

x -

Returns:

return the matrix-vector product b = Ax

plus

public SparseSquareMatrix plus(SparseSquareMatrix B)

return C = A + B

Parameters:

B -

Returns:

toString

public String toString()

Overrides:

toString in class Object