% Print out results obtained with BARCE

clear
clf

flag_L= input('Do you want to print out the log likelihoods? (0=no, 1=yes)');
flag_p_topo= input('Do you want to print out the weights for the topologies? (0=no, 1=yes)');
flag_branches= input('Do you want to print out the branch lengths? (0=no, 1=yes)');
flag_lambda= input('Do you want to print out lambda? (0=no, 1=yes)');

fontSize=15;

if flag_L
	load lpdfile.out;
	plot(lpdfile,'b-','LineWidth',2);
	set(gca,'Fontsize',fontSize);
end

if flag_p_topo
	lengthDNA=input('Type in length of the DNA sequences');
	load topol_prob.out;
	xMax=max(size(topol_prob,1),lengthDNA);
	subplot(3,1,1)
	plot(topol_prob(:,1),'b-','LineWidth',2);
	axis([1 xMax -0.1 1.1]);
	set(gca,'YTickMode','manual','YTick',[0 0.5 1],'XTickMode','manual','XTick',[floor(lengthDNA/4) floor(lengthDNA/2) floor(3*lengthDNA/4) lengthDNA])
	set(gca,'Fontsize',fontSize);
	ylabel('State 1');
	subplot(3,1,2)
	plot(topol_prob(:,2),'b-','LineWidth',2);
	axis([1 xMax -0.1 1.1]);
	set(gca,'YTickMode','manual','YTick',[0 0.5 1],'XTickMode','manual','XTick',[floor(lengthDNA/4) floor(lengthDNA/2) floor(3*lengthDNA/4) lengthDNA])
	set(gca,'Fontsize',fontSize);
	ylabel('State 2');
	subplot(3,1,3)
	plot(topol_prob(:,3),'b-','LineWidth',2);
	axis([1 xMax -0.1 1.1]);
	set(gca,'YTickMode','manual','YTick',[0 0.5 1],'XTickMode','manual','XTick',[floor(lengthDNA/4) floor(lengthDNA/2) floor(3*lengthDNA/4) lengthDNA])
	set(gca,'Fontsize',fontSize);
	ylabel('State 3');
end

if flag_branches
	load branch.out;
	subplot(3,1,1)
	plot(branch(:,1),'b-','LineWidth',2);
	set(gca,'Fontsize',fontSize);
	subplot(3,1,2)
	plot(branch(:,2),'b-','LineWidth',2);
	set(gca,'Fontsize',fontSize);
	subplot(3,1,3)
	plot(branch(:,3),'b-','LineWidth',2);
	set(gca,'Fontsize',fontSize);
end

if flag_lambda
	load lambda.out;
	%plot(lambda,'b.','markersize',5);
        plot(lambda,'b-','LineWidth',2);
	set(gca,'Fontsize',fontSize);
end