function y = testReadFromFile3 filename = fullfile(pwd,'test-data', 'l1v1-rules.xml'); m = TranslateSBML(filename); test = 77; Totalfail = 0; Totalfail = Totalfail + fail_unless(m.SBML_level == 1); Totalfail = Totalfail + fail_unless(m.SBML_version == 1); % /** % * % * % * % */ Totalfail = Totalfail + fail_unless( length(m.compartment) == 1); Totalfail = Totalfail + fail_unless( strcmp(m.compartment.name, 'cell')); 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, 'cell' )); Totalfail = Totalfail + fail_unless( m.species(1).initialAmount == 4); Totalfail = Totalfail + fail_unless( m.species(1).boundaryCondition == 0); Totalfail = Totalfail + fail_unless( strcmp( m.species(2).name, 's2' )); Totalfail = Totalfail + fail_unless( strcmp( m.species(2).compartment, 'cell' )); Totalfail = Totalfail + fail_unless( m.species(2).initialAmount == 2); Totalfail = Totalfail + fail_unless( m.species(2).boundaryCondition == 0); Totalfail = Totalfail + fail_unless( strcmp( m.species(3).name, 'x0' )); Totalfail = Totalfail + fail_unless( strcmp( m.species(3).compartment, 'cell' )); Totalfail = Totalfail + fail_unless( m.species(3).initialAmount == 1); Totalfail = Totalfail + fail_unless( m.species(3).boundaryCondition == 0); Totalfail = Totalfail + fail_unless( strcmp( m.species(4).name, 'x1' )); Totalfail = Totalfail + fail_unless( strcmp( m.species(4).compartment, 'cell' )); Totalfail = Totalfail + fail_unless( m.species(4).initialAmount == 0); Totalfail = Totalfail + fail_unless( m.species(4).boundaryCondition == 0); % /** % * % * % * % * % * % * % */ Totalfail = Totalfail + fail_unless( length(m.parameter) == 6); Totalfail = Totalfail + fail_unless( strcmp( m.parameter(1).name, 'k1' )); Totalfail = Totalfail + fail_unless( m.parameter(1).value == 1.2); Totalfail = Totalfail + fail_unless( strcmp( m.parameter(2).name, 'k2' )); Totalfail = Totalfail + fail_unless( m.parameter(2).value == 1000); Totalfail = Totalfail + fail_unless( strcmp( m.parameter(3).name, 'k3' )); Totalfail = Totalfail + fail_unless( m.parameter(3).value == 3000); Totalfail = Totalfail + fail_unless( strcmp( m.parameter(4).name, 'k4' )); Totalfail = Totalfail + fail_unless( m.parameter(4).value == 4.5); Totalfail = Totalfail + fail_unless( strcmp( m.parameter(5).name, 'k' )); Totalfail = Totalfail + fail_unless( m.parameter(5).value == 1); Totalfail = Totalfail + fail_unless( strcmp( m.parameter(6).name, 't' )); Totalfail = Totalfail + fail_unless( m.parameter(6).value == 1); % /** % * % * % * % * % * % * % */ Totalfail = Totalfail + fail_unless( length(m.rule) == 4); Totalfail = Totalfail + fail_unless( strcmp( m.rule(1).typecode, 'SBML_PARAMETER_RULE' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(1).type, 'scalar' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(1).name, 't' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(1).formula, 's1+s2' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(2).typecode, 'SBML_PARAMETER_RULE' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(2).type, 'scalar' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(2).name, 'k' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(2).formula, 'k3/k2' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(3).typecode, 'SBML_SPECIES_CONCENTRATION_RULE' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(3).type, 'scalar' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(3).species, 's2' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(3).formula, 'k*t/(1+k)' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(4).typecode, 'SBML_SPECIES_CONCENTRATION_RULE' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(4).type, 'scalar' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(4).species, 's1' )); Totalfail = Totalfail + fail_unless( strcmp( m.rule(4).formula, 't-s2' )); % /** % * % * ... % * ... % * % */ Totalfail = Totalfail + fail_unless( length(m.reaction) == 2); Totalfail = Totalfail + fail_unless( strcmp(m.reaction(1).name, 'j1')); 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, 'j3')); Totalfail = Totalfail + fail_unless( m.reaction(2).reversible ~= 0); Totalfail = Totalfail + fail_unless( m.reaction(2).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(2).reactant) == 1); Totalfail = Totalfail + fail_unless( length(m.reaction(2).product) == 1); Totalfail = Totalfail + fail_unless( strcmp(m.reaction(2).reactant.species, 's2')); 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, 'k4*s2')); disp('Testing readFromFile3:'); 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;