function [c1, c2] = alignCoords(crd1, s1, crd2, s2)

%ALIGNCOORDS   Align coordinates of amino acids in correspondece with 
%              the sequence alignment.
%  [C1, C2] = alignCoords(CRD1, S1, CRD2, S2),  where CRD1 and CRD2
%  are the original coordinate matrices, S1 and S2 are the aligned 
%  sequences, and C1 and C2 are coordinate matrices corresponding to
%  the sequence alignment of s1 and s2.

if (length(s1) ~= length(s2))
   error('Aligned sequences must have the same length');
end

c1 = [];  index1 = 0;
c2 = [];  index2 = 0;
j  = 0;   n = length(s1);
for i=1:n
   if (s1(i) ~= '-' & s2(i) ~= '-')   % Two amino acids aligned against each other
      index1 = index1 + 1;            % Align the corresponding coordinates
      index2 = index2 + 1;            %   against one another
      j = j + 1;                      % j is the current length of the either 
      c1(j, :) = crd1(index1, :);     %   aligned coordinate matrix
      c2(j, :) = crd2(index2, :);
   elseif (s1(i) == '-')              % Amino acid is s2 aligned against gap in s1
      index2 = index2 + 1;            % Skip corresponding coordinate in s2
   else                               % Amino acid is s1 aligned against gap in s2
      index1 = index1 + 1;            % Skip corresponding coordinate in s1
   end
end