function hash = calculateMD5Hash(filename)
% CALCULATEMD5HASH calculate a MD5 hash of a file
%
% This functionality is built-in into Octave but uses Java in MATLAB.

    switch getEnvironment
        case 'Octave'
            hash = md5sum(filename);

        case 'MATLAB'
            % There are some MD5 implementations in MATLAB, but those
            % tend to be slow and licensing is unclear.
            % Rolling our own implementation is unwanted, especially since this
            % is a  cryptographic hash, even though its security has been
            % broken. Instead we make use of the Java libraries.
            % Unless the "-nojvm" flag is specified, this should work well.
            
            MD5 = java.security.MessageDigest.getInstance('MD5');
                        
            % Open the file
            fid = fopen(filename, 'r');
            
            % Make sure fid is closed
            finally_close = onCleanup(@()fclose(fid));
            
            % Faster file digest based on code by Jan Simon as in 
            % http://www.mathworks.com/matlabcentral/fileexchange/31272-datahash
            data = fread(fid, '*uint8');
            MD5.update(data);
            
            hash = reshape(dec2hex(typecast(MD5.digest(),'uint8')).', 1, 32);
    end

    hash = lower(hash);
end