my @actual_mat = (

   [ 0.994704478, 0.000882587, 0.000882587, 0.000882587, 0.002647761],
   [ 0.005270463, 0.989459074, 0.002635231, 0.002635231, 0.000000000],
   [ 0.000000000, 0.000000000, 0.005282977, 0.000000000, 0.000000000].
   [ 0.000000000, 0.000000000, 0.000000000, 1.000000000, 0.000000000],
   [ 0.000000000, 0.000000000, 0.000000000, 0.000000000, 1.000000000]
);

# It is simply done by assigning the value in @real_value given
# the corresponding (@row,@index) as coordinate;
# e.g. to assign $real_value[-1] into  
# $actual_mat[$row_index[-1]-1,$col_index[-1]-1);