%%%%%%% 
% bioadjmat.m
% Author: Lance Harden, Davidson College
% June 2006
% 
% Description: Bioadjmat creates an adjacency matrix for all signed
% permutations of length k that are molecularly unique. The input s allows
% the user to choose between 1 or 2 spatulas (prefix sorting by reversals
% vs. sorting by reversals).

function [adj] = bioadjmat(k,s)

if nargin < 2, s = 2; end

B = bioperms(k);
b = length(B);
adj = zeros(b);

if s == 1
    for j = 1:b
        P = B(j,:);
        for FL = 1:k
            range = FL - 1;
            G = [fliplr(P(1:range)) P(FL:k)];
            for f = 1:range
                G(f) = -G(f);
            end
            comp = -(fliplr(G));
            for i = 1:b
                if ( all(G == B(i,:)) || all(comp == B(i,:)) )
                    adj(i,j) = 1;
                    break
                end
            end
        end
    end
else
    for j = 1:b
        P = B(j,:);
        for FL = 1:k
            range = FL - 1;
            for t = 1:(k+1-FL)
                G = [P(1:t-1) fliplr(P(t:t+range)) P(t+FL:k)];
                for f = t:t+range
                    G(f) = -G(f);
                end
                comp = -(fliplr(G));
                for i = 1:b
                    if ( all(G == B(i,:)) || all(comp == B(i,:)) )
                        adj(i,j) = 1;
                        break
                    end
                end
            end
        end
    end
end