xFlankingPairs identifies nucleotides on the same strand which make
0001 % xFlankingPairs identifies nucleotides on the same strand which make 0002 function [File] = xFlankingPairs(File) 0003 0004 E = triu(fix(abs(File.Edge))==1) .* (File.Range == 0); % nested cWW's, i < j 0005 X = (File.Range == 0) .* (abs(File.Edge) > 0) .* (abs(File.Edge) < 15); 0006 0007 H = sparse(zeros(File.NumNT,File.NumNT)); % to indicate flanks 0008 0009 [i,j] = find(E); % indices of NT's making nested cWW's 0010 0011 a = [i; j]; % all indices of nested cWW pairs 0012 0013 a = sort(a); % put them into one list 0014 0015 for k = 1:(length(a)-1), % run through all NT making nested cWW 0016 if a(k+1) - a(k) > 1, % where there is a gap in the number, 0017 H(a(k),a(k+1)) = 1; % these two flank something 0018 end 0019 end 0020 0021 H = H + H'; % symmetrize H 0022 0023 File.Flank = H; % store 0024