Package 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:

  • Constructor Details

    • SparseSquareMatrix

      public SparseSquareMatrix(int N)
      initialize an N-by-N matrix of all 0s
      Parameters:
      N - - size

  • Method Details

    • 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