xReduceOverlap

0001 
0002 function [Candidates, Discrepancy] = xReduceOverlap(Candidates, Discrepancy)
0003 
0004 N = length(Candidates(1,:)) - 1;                 % number of nucleotides
0005 
0006 %fprintf('%6d candidates after %2d exclusions\n', length(Candidates(:,1)),0);
0007 drawnow
0008 
0009 a = 1;
0010 
0011 for a=1:N,
0012   i = [a:N 1:(a-1)];
0013     
0014   [Candidates, Discrepancy] = xExcludeOverlap2(Candidates, Discrepancy, i);
0015 
0016 %  fprintf('%6d candidates after %2d exclusions\n', length(Candidates(:,1)),a);
0017 
0018   drawnow
0019 end
0020 
0021 for a=1:N,
0022   i = [a:-1:1 N:-1:(a+1)];
0023     
0024   [Candidates, Discrepancy] = xExcludeOverlap2(Candidates, Discrepancy, i);
0025 
0026   %fprintf('%6d candidates after %2d exclusions\n', length(Candidates(:,1)),a+N);
0027   drawnow
0028 end
0029 
0030 return
0031 
0032 while a < 3000,
0033   r = rand(1,N);
0034   [y,i] = sort(r);                    % i is a random permutation
0035     
0036   [Candidates, Discrepancy] = xExcludeOverlap2(Candidates, Discrepancy, i);
0037 
0038   [a size(Candidates)]
0039   drawnow
0040 
0041   a = a + 1;
0042 end