function y = testReadFromFile1
filename = fullfile(pwd,'test-data', 'l1v1-branch.xml');
notes1 = sprintf('%s\n %s\n %s\n %s\n %s\n %s\n %s\n %s\n%s', ...
'', ...
'', ...
'Simple branch system.
', ...
'The reaction looks like this:
', ...
'reaction-1: X0 -> S1; k1*X0;
', ...
'reaction-2: S1 -> X1; k2*S1;
', ...
'reaction-3: S1 -> X2; k3*S1;
', ...
'', ...
'');
m = TranslateSBML(filename);
test = 70;
Totalfail = 0;
Totalfail = Totalfail + fail_unless(m.SBML_level == 1);
Totalfail = Totalfail + fail_unless(m.SBML_version == 1);
Totalfail = Totalfail + fail_unless(strcmp(m.name,'Branch'));
Totalfail = Totalfail + fail_unless(strcmp(m.notes, notes1));
% /**
% *
% *
% *
% */
Totalfail = Totalfail + fail_unless( length(m.compartment) == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.compartment.name, 'compartmentOne'));
Totalfail = Totalfail + fail_unless( m.compartment.volume == 1);
% /**
% *
% *
% *
% *
% *
% *
% */
Totalfail = Totalfail + fail_unless( length(m.species) == 4);
Totalfail = Totalfail + fail_unless( strcmp( m.species(1).name, 'S1' ));
Totalfail = Totalfail + fail_unless( strcmp( m.species(1).compartment, 'compartmentOne' ));
Totalfail = Totalfail + fail_unless( m.species(1).initialAmount == 0);
Totalfail = Totalfail + fail_unless( m.species(1).boundaryCondition == 0);
Totalfail = Totalfail + fail_unless( strcmp( m.species(2).name, 'X0' ));
Totalfail = Totalfail + fail_unless( strcmp( m.species(2).compartment, 'compartmentOne' ));
Totalfail = Totalfail + fail_unless( m.species(2).initialAmount == 0);
Totalfail = Totalfail + fail_unless( m.species(2).boundaryCondition == 1);
Totalfail = Totalfail + fail_unless( strcmp( m.species(3).name, 'X1' ));
Totalfail = Totalfail + fail_unless( strcmp( m.species(3).compartment, 'compartmentOne' ));
Totalfail = Totalfail + fail_unless( m.species(3).initialAmount == 0);
Totalfail = Totalfail + fail_unless( m.species(3).boundaryCondition == 1);
Totalfail = Totalfail + fail_unless( strcmp( m.species(4).name, 'X2' ));
Totalfail = Totalfail + fail_unless( strcmp( m.species(4).compartment, 'compartmentOne' ));
Totalfail = Totalfail + fail_unless( m.species(4).initialAmount == 0);
Totalfail = Totalfail + fail_unless( m.species(4).boundaryCondition == 1);
%
% /**
% *
% * ...
% * ...
% * ...
% *
% */
Totalfail = Totalfail + fail_unless( length(m.reaction) == 3);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(1).name, 'reaction_1'));
Totalfail = Totalfail + fail_unless( m.reaction(1).reversible == 0);
Totalfail = Totalfail + fail_unless( m.reaction(1).fast == 0);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(2).name, 'reaction_2'));
Totalfail = Totalfail + fail_unless( m.reaction(2).reversible == 0);
Totalfail = Totalfail + fail_unless( m.reaction(2).fast == 0);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(3).name, 'reaction_3'));
Totalfail = Totalfail + fail_unless( m.reaction(3).reversible == 0);
Totalfail = Totalfail + fail_unless( m.reaction(3).fast == 0);
%
% /**
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% */
%
Totalfail = Totalfail + fail_unless( length(m.reaction(1).reactant) == 1);
Totalfail = Totalfail + fail_unless( length(m.reaction(1).product) == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(1).reactant.species, 'X0'));
Totalfail = Totalfail + fail_unless( m.reaction(1).reactant.stoichiometry == 1);
Totalfail = Totalfail + fail_unless( m.reaction(1).reactant.denominator == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(1).product.species, 'S1'));
Totalfail = Totalfail + fail_unless( m.reaction(1).product.stoichiometry == 1);
Totalfail = Totalfail + fail_unless( m.reaction(1).product.denominator == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(1).kineticLaw.formula, 'k1*X0'));
Totalfail = Totalfail + fail_unless(length(m.reaction(1).kineticLaw.parameter) == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(1).kineticLaw.parameter.name, 'k1'));
Totalfail = Totalfail + fail_unless( m.reaction(1).kineticLaw.parameter.value == 0);
%
%
% /**
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% */
Totalfail = Totalfail + fail_unless( length(m.reaction(2).reactant) == 1);
Totalfail = Totalfail + fail_unless( length(m.reaction(2).product) == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(2).reactant.species, 'S1'));
Totalfail = Totalfail + fail_unless( m.reaction(2).reactant.stoichiometry == 1);
Totalfail = Totalfail + fail_unless( m.reaction(2).reactant.denominator == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(2).product.species, 'X1'));
Totalfail = Totalfail + fail_unless( m.reaction(2).product.stoichiometry == 1);
Totalfail = Totalfail + fail_unless( m.reaction(2).product.denominator == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(2).kineticLaw.formula, 'k2*S1'));
Totalfail = Totalfail + fail_unless(length(m.reaction(2).kineticLaw.parameter) == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(2).kineticLaw.parameter.name, 'k2'));
Totalfail = Totalfail + fail_unless( m.reaction(2).kineticLaw.parameter.value == 0);
%
% /**
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% *
% */
Totalfail = Totalfail + fail_unless( length(m.reaction(3).reactant) == 1);
Totalfail = Totalfail + fail_unless( length(m.reaction(3).product) == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(3).reactant.species, 'S1'));
Totalfail = Totalfail + fail_unless( m.reaction(3).reactant.stoichiometry == 1);
Totalfail = Totalfail + fail_unless( m.reaction(3).reactant.denominator == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(3).product.species, 'X2'));
Totalfail = Totalfail + fail_unless( m.reaction(3).product.stoichiometry == 1);
Totalfail = Totalfail + fail_unless( m.reaction(3).product.denominator == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(3).kineticLaw.formula, 'k3*S1'));
Totalfail = Totalfail + fail_unless(length(m.reaction(3).kineticLaw.parameter) == 1);
Totalfail = Totalfail + fail_unless( strcmp(m.reaction(3).kineticLaw.parameter.name, 'k3'));
Totalfail = Totalfail + fail_unless( m.reaction(3).kineticLaw.parameter.value == 0);
disp('Testing readFromFile1:');
disp(sprintf('Number tests: %d', test));
disp(sprintf('Number fails: %d', Totalfail));
disp(sprintf('Pass rate: %d%%\n', ((test-Totalfail)/test)*100));
if (Totalfail == 0)
y = 0;
else
y = 1;
end;
function y = fail_unless(arg)
if (~arg)
y = 1;
else
y = 0;
end;