function S = readScoreMatrix(matrixFileName)

%READSCOREMATRIX   Reads a scoring matrix from a file
% S = readScoreMatrix(matrixFileName) reads a scoring matrix
%   from a file.  The score matrix must contain NxN entries,
%   and must be symmetric.

% Read entries from the file containing the matrix
fid = fopen(matrixFileName, 'r');
L = fgetl(fid);
i = 0;
M = [];
while (isstr(L))     % Read until L is not empty
  i = i+1;
  M(i,:) = sscanf(L, '%f', [1, inf]);
  L = fgetl(fid);
end

% Ensure that the scoring matrix is symmetric
epsilon = 0.001;    % Round-off error
if (size(M,1) ~= size(M,2) | norm(triu(M)-tril(M)') > epsilon)
  error('The scoring matrix must be symmetric');
end

S = M;