function a = setTransitionProbabilities
% setTransitionProbabilities this function sets the transition probabilites
% of the model. Values are hard-coded in the function body
N = 4;
a = zeros(N);

% state 1 (intergenic region or non-coding region)
a(1,1) = 1/150;
a(1,2) = (1-a(1,1));
% a(1,5) = (1-a(1,1))/2;

% state 2 (direct start codon)
a(2,3) = 1;

% state 3 (direct coding region state)
a(3,4) = 1;

% state 4 (direct stop codon)
a(4,1) = 1;

% % state 5 (reverse stop codon)
% a(5,6) = 1;
% 
% % state 6 (reverse coding region state)
% a(6,7) = 1;
% 
% % state 7 (reverse start codon)
% a(7,1) = 1;

end
