clear all, close all

%%  read in the data
[data,headerNames]=tblread('system_example_nf.gdat'); % this is a function from NFsim
[x,y]=size(data);

h1=figure(); % create a figure in matlab
subplot(2,2,[1;2]) % divide the figure, so that multiple graphs can be visualized in one figure
semilogx(data(:,1),data(:,2:y),'LineWidth',2)
legend(headerNames(2:y,:)) % create a legend
title('Molecules of the system') % give the graph a title
xlabel(headerNames(1,:)) % label the x-axis
ylabel('Molecules') % label the y-axis

%% analyze NFdump
baseDirectory='dumpDir_example_dump';
systemName='system_example';

[results]=readNFdump(baseDirectory,systemName); % this is a function from NFsim

amount=length(results);
TIME = zeros(amount,1);
for i=1:amount
    index=i;
    TIME(index)=results(index).time; % extract the time points
end
[names] = getMolTypeNames(results,TIME(1)); % this is a function from NFsim
% names(1)=Protein1
% names(2)=Protein2
% names(3)=Inducer

%% use the three functions for complex size analysis
[avgSize1, totalMolecules1, totalComplexes1] = getAvgComplexSize(results,names);
[avgSize2, totalMolecules2, totalComplexes2, sizeOneCount] = getAvgComplexSizeLargerThanOne(results,names);
[avgSize3, totalMolecules3, totalComplexes3] = getAvgComplexSizeAll(results);

% [avgSize2, totalMolecules2, totalComplexes2, sizeOneCount] = getAvgComplexSizeLargerThanOne(results,names);
subplot(2,2,3)
semilogx(TIME,totalComplexes2,TIME,totalComplexes3,TIME,sizeOneCount,'LineWidth',2) % 'Color',[0 0 128/255],'LineWidth',2)
legend('Complexes method 1', 'Complexes mthod 2','Single Molecules') % make a legend
title('Total Amount of Complexes') % give the graph a title
xlabel('Time [s]') % label the x-axis
ylabel('Molecules') % label the y-axis


subplot(2,2,4)
semilogx(TIME,avgSize1,TIME,avgSize3,'LineWidth',2)% 'Color',[0 0 128/255],'LineWidth',2)
legend('Size method 1', 'Size method 3') % make a legend
title('Average Complex Size') % give the graph a title
xlabel('Time [s]') % label the x-axis
ylabel('Molecules') % label the y-axis

%% save separate figures
h2=figure();
semilogx(data(:,1),data(:,2:y),'LineWidth',2)
legend(headerNames(2:y,:)) % create a legend
title('Molecules of the system')
xlabel(headerNames(1,:))
ylabel('Molecules')

saveas(h2,'system_example_a.png')

h3=figure();
semilogx(TIME,totalComplexes1,TIME,totalComplexes3,TIME,sizeOneCount,'LineWidth',2) % 'Color',[0 0 128/255],'LineWidth',2)
legend('Complexes method 1', 'Complexes mthod 3','Single Molecules') % make a legend
title('Total Amount of Complexes') % give the graph a title
xlabel('Time [s]') % label the x-axis
ylabel('Molecules') % label the y-axis

saveas(h3,'system_example_b.png')

h4=figure();
semilogx(TIME,avgSize1,TIME,avgSize3,'LineWidth',2)% 'Color',[0 0 128/255],'LineWidth',2)
legend('Size method 1', 'Size method 3') % make a legend
title('Average Complex Size') % give the graph a title
xlabel('Time [s]') % label the x-axis
ylabel('Molecules') % label the y-axis

saveas(h4,'system_example_c.png')