%This function runs through an array describing state space and
%finds the paths and duration of it. It will return an array of 
%actual path durations from one metastable state to other.
function [X,pathsAB,pathsBA]=TransitionPaths(S)
size_s = size(S);
X=[];
pathsAB = [[]];
pathsBA = [[]];
pTP=0;
i=1;
j=1;
k1=1;
k2=1;
while(S(i) == 0)
    i = i+1;
end
curr_state = S(i)
s_index = i
i=i+1;
while(i<=size_s(1))
    if(S(i)==0)
        i = i+1;
    elseif S(i) == curr_state
        curr_state = S(i);
        s_index = i;
        i = i+1;
    elseif S(i) ~= curr_state
        %a path has been found
        X(j) = i-s_index;
        if S(s_index) == 1
            pathsAB(k1,1) = s_index;
            pathsAB(k1,2) = i;
            k1 = k1+1;
            %%%%X(j) = i-s_index;
            %%%%j = j+1;
        elseif S(s_index) == 2
            pathsBA(k2,2) = s_index;
            pathsBA(k2,1) = i;
            k2 = k2+1;
        end
%         if X(j) == 1
%             i
%             S(i)
%             S(i-1)
%         end
        j = j+1;
        curr_state = S(i);
        s_index = i;
        i = i+1;
    end
end