END_TEST
START_TEST(test_FbcExtension_create_and_write_new_geneassociation
)
{
FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 2);
// create the document
SBMLDocument document(sbmlns);
document.setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.setConsistencyChecks(LIBSBML_CAT_MODELING_PRACTICE, false);
// create the Model
Model* model = document.createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("compartment");
compartment->setConstant(true);
compartment->setSize(1);
// create the Species
Species* species = model->createSpecies();
species->setId("Node1");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species = model->createSpecies();
species->setId("Node2");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
Reaction* reaction = model->createReaction();
reaction->setId("J0");
reaction->setReversible(false);
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("Node0");
reactant->setStoichiometry(1);
SpeciesReference* product = reaction->createProduct();
product->setSpecies("Node1");
product->setStoichiometry(1);
// use fbc
FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
fail_unless(mplugin != NULL);
FluxBound* bound = mplugin->createFluxBound();
bound->setId("bound1");
bound->setReaction("J0");
bound->setOperation("equal");
bound->setValue(10);
Objective* objective = mplugin->createObjective();
objective->setId("obj1");
objective->setType("maximize");
FluxObjective* fluxObjective = objective->createFluxObjective();
fluxObjective->setReaction("J0");
fluxObjective->setCoefficient(1);
FbcReactionPlugin* rplug = dynamic_cast<FbcReactionPlugin*>(reaction->getPlugin("fbc"));
fail_unless(rplug != NULL);
GeneProductAssociation * ga = rplug->createGeneProductAssociation();
ga->setId("ga1");
ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
fail_unless(ga->getAssociation() != NULL);
fail_unless(mplugin->getNumGeneProducts() == 5);
ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
fail_unless(ga->getAssociation() != NULL);
fail_unless(mplugin->getNumGeneProducts() == 5);
delete sbmlns;
}
END_TEST
START_TEST(test_FbcAssociation_parseFbcInfixAssociation_strange_labels)
{
const char* model1 =
"<?xml version='1.0' encoding='UTF-8'?>"
"<sbml xmlns:html='http://www.w3.org/1999/xhtml' xmlns='http://www.sbml.org/sbml/level3/version1/core' xmlns:fbc='http://www.sbml.org/sbml/level3/version1/fbc/version2' level='3' version='1' fbc:required='false'>"
" <model id='M' name='E' timeUnits='dimensionless' fbc:strict='false'>"
" <listOfCompartments>"
" <compartment id=\"comp1\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>"
" </listOfCompartments>"
" <listOfSpecies>"
" <species id=\"S\" compartment=\"comp1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" fbc:charge=\"2\" fbc:chemicalFormula=\"S20\"/>"
" </listOfSpecies>"
" <listOfReactions>"
" <reaction id=\"R1\" reversible=\"false\" fast=\"false\" fbc:lowerFluxBound=\"low\" fbc:upperFluxBound=\"up\">"
" <listOfReactants>"
" <speciesReference species=\"S1\" stoichiometry=\"1\" constant=\"true\"/>"
" </listOfReactants>"
" </reaction>"
" </listOfReactions>"
" </model>"
"</sbml>"
;
const char* expected =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<sbml xmlns:html=\"http://www.w3.org/1999/xhtml\" xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" xmlns:fbc=\"http://www.sbml.org/sbml/level3/version1/fbc/version2\" level=\"3\" version=\"1\" fbc:required=\"false\">\n"
" <model id=\"M\" name=\"E\" timeUnits=\"dimensionless\" fbc:strict=\"false\">\n"
" <listOfCompartments>\n"
" <compartment id=\"comp1\" spatialDimensions=\"3\" size=\"1\" constant=\"true\"/>\n"
" </listOfCompartments>\n"
" <listOfSpecies>\n"
" <species id=\"S\" compartment=\"comp1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\" fbc:charge=\"2\" fbc:chemicalFormula=\"S20\"/>\n"
" </listOfSpecies>\n"
" <listOfReactions>\n"
" <reaction id=\"R1\" reversible=\"false\" fast=\"false\" fbc:lowerFluxBound=\"low\" fbc:upperFluxBound=\"up\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"S1\" stoichiometry=\"1\" constant=\"true\"/>\n"
" </listOfReactants>\n"
" <fbc:geneProductAssociation fbc:id=\"gg1\">\n"
" <fbc:and>\n"
" <fbc:geneProductRef fbc:geneProduct=\"gp_g__DOT__p\"/>\n"
" <fbc:geneProductRef fbc:geneProduct=\"gp___ONE__sd\"/>\n"
" </fbc:and>\n"
" </fbc:geneProductAssociation>\n"
" </reaction>\n"
" </listOfReactions>\n"
" <fbc:listOfGeneProducts>\n"
" <fbc:geneProduct fbc:id=\"gp_g__DOT__p\" fbc:label=\"g.p\"/>\n"
" <fbc:geneProduct fbc:id=\"gp___ONE__sd\" fbc:label=\"1sd\"/>\n"
" </fbc:listOfGeneProducts>\n"
" </model>\n"
"</sbml>\n"
;
std::string infix = "(g.p and 1sd)";
SBMLDocument* doc = readSBMLFromString(model1);
fail_unless(doc->getModel() != NULL);
FbcModelPlugin* fbc = dynamic_cast<FbcModelPlugin*>(doc->getModel()->getPlugin("fbc"));
fail_unless(fbc != NULL);
fail_unless(fbc->getNumGeneProducts() == 0);
Reaction * r = doc->getModel()->getReaction(0);
fail_unless(r != NULL);
FbcReactionPlugin * rplug = dynamic_cast<FbcReactionPlugin*>(r->getPlugin("fbc"));
fail_unless (rplug != NULL);
fail_unless(rplug->isSetGeneProductAssociation() == false);
GeneProductAssociation* gpa = rplug->createGeneProductAssociation();
gpa->setId("gg1");
FbcAssociation * fa = FbcAssociation::parseFbcInfixAssociation(infix, fbc);
fail_unless(fa->isFbcAnd() == true);
gpa->setAssociation(fa);
fail_unless(rplug->isSetGeneProductAssociation() == true);
fail_unless(fbc->getNumGeneProducts() == 2);
GeneProduct* gp = fbc->getGeneProduct(0);
fail_unless (gp->isSetId() == true);
fail_unless (gp->isSetLabel() == true);
FbcAssociation * fa_retrieved = gpa->getAssociation();
fail_unless(fa_retrieved->isFbcAnd() == true);
std::string out = fa_retrieved->toInfix();
// if it goes back to infix surely it should be the same infix that it started as
fail_unless(fa_retrieved->toInfix() == infix);
//GeneProductRef * gpref = dynamic_cast<GeneProductRef *>(gpa->getAssociation());
//fail_unless(gpref->isSetGeneProduct() == true);
//fail_unless(gpref->getGeneProduct() == gp->getId());
char * char_doc = writeSBMLToString(doc);
fail_unless(equals(expected, char_doc));
safe_free((void*)(char_doc));
delete fa;
delete doc;
}
