Legend and plot for scaffold-substrate system (Hammerhead/Ribozyme).

@Ternary_model/plot_sim.m

@@ -16,6 +16,7 @@ if strcmp(mode, 'mov')
     for i = 1:nth:length(T.t)
         cla;
         axis([0, T.system_size, 0, max(T.sol(:))]);
+        xlim([0, 10]);
         ax = gca; ax.FontSize = 12;
         xlabel('position'); ylabel('probability [not normalized]');
         plot(T.x, T.phi_tot(T.x, T.a, T.b, T.e, T.u0, T.t(i)*T.v),...
@@ -24,10 +25,12 @@ if strcmp(mode, 'mov')
             plot(T.x, T.sol(i, :), 'LineWidth', 2);
         elseif length(size(T.sol))==3
             plot(T.x, T.sol(i, :, 1), 'LineWidth', 2, 'Color', color);
-            plot(T.x, T.sol(i, :, 2), 'LineWidth', 2, 'Color', 'k');
+            plot(T.x, T.sol(i, :, 2), 'LineWidth', 2, 'Color', 'g');
+            legend('Droplet scaffold', 'Substrate', 'Cleaved product');
         end
         text(abs(-T.a+2), 0.7, num2str(T.t(i)));
-        shg; pause();
+        shg;
+        pause();
 %         print([num2str(i),'.png'],'-dpng')
     end
 elseif strcmp(mode, 'plot')