END_TEST
START_TEST (test_infer_localParam_fromReaction)
{
string filename(TestDataDirectory);
filename += "inferUnits-3.xml";
SBMLDocument* d = readSBMLFromFile(filename.c_str());
fail_unless(d != NULL);
LocalParameter * p = d->getModel()->getReaction(1)->
getKineticLaw()->getLocalParameter("k2");
fail_unless(p->isSetUnits() == false);
p->setCalculatingUnits(true);
UnitDefinition *ud = p->getDerivedUnitDefinition();
fail_unless(ud->getNumUnits() == 1);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == -1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_SECOND);
delete ud;
// TO DO make the units converter do local parameters;
//fail_unless(d->getModel()->getNumUnitDefinitions() == 3);
//
//SBMLInferUnitsConverter * units = new SBMLInferUnitsConverter();
//units->setDocument(d);
//fail_unless (units->convert() == LIBSBML_OPERATION_SUCCESS);
//kl = d->getModel()->getReaction(1)->getKineticLaw();
//fail_unless(kl->getLocalParameter("k2")->isSetUnits() == true);
//fail_unless(kl->getLocalParameter("k2")->getUnits() == "per_time");
//delete units;
delete d;
}
void updateKineticLawFromBound(Reaction* reaction, FluxBound* current)
{
if (reaction == NULL || current == NULL)
return;
const string operation = current -> getOperation();
KineticLaw *law = reaction->getKineticLaw();
LocalParameter* LB = law->getLocalParameter("LOWER_BOUND");
LocalParameter* UB = law->getLocalParameter("UPPER_BOUND");
if (operation == "less" || operation == "lessEqual" || operation == "equal")
{
UB->setValue(current->getValue());
}
if (operation == "greater" || operation == "greaterEqual" || operation == "equal")
{
LB->setValue(current->getValue());
}
}
END_TEST
START_TEST (test_WriteL3SBML_KineticLaw_ListOfParameters)
{
const char* expected =
"<kineticLaw>\n"
" <listOfLocalParameters>\n"
" <localParameter id=\"n\" value=\"1.2\"/>\n"
" </listOfLocalParameters>\n"
"</kineticLaw>";
KineticLaw *kl = D->createModel()->createReaction()->createKineticLaw();
LocalParameter *p = kl->createLocalParameter();
p->setId("n");
p->setValue(1.2);
char* sbml = kl->toSBML();
fail_unless( equals(expected, sbml) );
safe_free(sbml);
}
void setObjectiveCoefficient(FbcModelPlugin* plugin, Model* model)
{
if (plugin == NULL || model == NULL)
return;
Objective* obj = plugin->getActiveObjective();
if (obj == NULL)
return;
for (unsigned int i = 0; i < obj->getNumFluxObjectives(); ++i)
{
FluxObjective* fluxObj = obj->getFluxObjective(i);
if (fluxObj == NULL)
continue;
Reaction* reaction = model->getReaction(fluxObj->getReaction());
if (reaction == NULL)
continue;
KineticLaw* law = reaction->getKineticLaw();
if (law == NULL)
continue;
LocalParameter* param = law->getLocalParameter("OBJECTIVE_COEFFICIENT");
param->setValue(fluxObj->getCoefficient());
}
}
void createKineticLawForReaction(Reaction* reaction)
{
if (reaction == NULL)
return;
reaction->unsetKineticLaw();
KineticLaw *law = reaction->getKineticLaw();
if (law == NULL)
{
law = reaction->createKineticLaw();
LocalParameter* fluxValue = law->createLocalParameter();
fluxValue->initDefaults();
fluxValue->setId("FLUX_VALUE");
fluxValue->setValue(0);
fluxValue->setUnits("dimensionless");
law->setMath(SBML_parseFormula("FLUX_VALUE"));
}
LocalParameter* LB = law->getLocalParameter("LOWER_BOUND");
if (LB == NULL)
{
LB = law->createLocalParameter();
LB->initDefaults();
LB->setId("LOWER_BOUND");
LB->setUnits("dimensionless");
LB->setValue(-std::numeric_limits<double>::infinity());
}
LocalParameter* UB = law->getLocalParameter("UPPER_BOUND");
if (UB == NULL)
{
UB = law->createLocalParameter();
UB->initDefaults();
UB->setId("UPPER_BOUND");
UB->setUnits("dimensionless");
LB->setValue(std::numeric_limits<double>::infinity());
}
LocalParameter* param = law->getLocalParameter("OBJECTIVE_COEFFICIENT");
if (param == NULL)
{
param = law->createLocalParameter();
param->initDefaults();
param->setId("OBJECTIVE_COEFFICIENT");
param->setUnits("dimensionless");
param->setValue(0);
}
}
