clear all; 
close all;

format long e; 

delete time_v2.dat
delete sg0_v2.dat

global pulse tau_on tau_off

% x0 = bioclock_core_v3(); % initial conditions
t_end = 100;
error = 1e-6;


% x0(1) = 1;  % change sg0 to single pulse ... this can be changed later 
options = odeset('RelTol',error,'AbsTol',error); % options

% [time_sim x_sim] = ode23s(@bioclock_core_v3,[0,t_end], x0, options);

% figure;
% plot(time_sim,x_sim);
% hold on;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%% intermitent pulsing
x0 = bioclock_core_v3(); % initial conditions again
%t_end = 100;
pulse = 1;
tau_on = 5;
tau_off = 20; 

[time_sim2 x_sim2] = ode23s(@bioclock_core_v3,[0 t_end], x0, options);


%%% load data files
%%%%% pulsing plots
time_v2 = load('time_v2.dat');
sg0_v2 = load('sg0_v2.dat');


%%%%%%% PLOTTING TEMPLATE
% figure;
% plot(Corner1_time,Corner1_c_OPG,'r');
% hold on;
% plot(Corner2_time,Corner2_c_OPG,'g');
% plot(Corner3_time,Corner3_c_OPG,'b');
% plot(Corner4_time,Corner4_c_OPG,'k');
% title('Plot of OPG concentration', 'Fontsize', 12);
% xlabel('t [days]');
% ylabel('OPG [pM]');
% legend('Corner1','Corner2','Corner3', 'Corner4',1);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
figure;
plot(time_sim2,x_sim2(:,2),'r');
hold on;
title('Plot of On1 concentration', 'Fontsize', 12);
xlabel('t ');
ylabel('On1 [M]');
legend('On1',1);

figure;
plot(time_sim2,x_sim2(:,7),'g');
hold on;
title('Plot of B1 concentration', 'Fontsize', 12);
xlabel('t ');
ylabel('B1 [M]');
legend('B1',1);
% 
% 
figure;
plot(time_v2,sg0_v2);
hold on;
title('Plot of Sg0 pulse','Fontsize',12);
xlabel('t');
ylabel('Sg0 pulse');
legend('Sg0',1);
% 
figure;
plot(time_sim2,x_sim2(:,1),'r');
hold on;
title('Plot of On0 concentration', 'Fontsize', 12);
xlabel('t ');
ylabel('On0 [M]');
legend('On0',1);
% 
figure;
plot(time_sim2,x_sim2(:,6),'r');
hold on;
title('Plot of Sg1 concentration', 'Fontsize', 12);
xlabel('t ');
ylabel('Sg1 [M]');
legend('Sg1',1);

% figure;
% plot(time_sim2,x_sim2(:,3),'r');
% hold on;
% title('Plot of Tr0 concentration', 'Fontsize', 12);
% xlabel('t ');
% ylabel('Tr0 [M]');
% legend('Tr0',1);