END_TEST
START_TEST(test_FbcExtension_convert_and_write)
{
string file(TestDataDirectory);
file += "/fbc_ga_example.xml";
SBMLDocument* document = readSBMLFromFile(file.c_str());
document->printErrors();
fail_unless(document->getNumErrors(LIBSBML_SEV_ERROR) == 0);
fail_unless(document->getModel() != NULL);
// convert to v2
{
ConversionProperties props;
props.addOption("convert fbc v1 to fbc v2", true);
props.addOption("strict", true);
int result = document->convert(props);
// ensure that all is well with the model
fail_unless(result == LIBSBML_OPERATION_SUCCESS);
fail_unless(document->getLevel() == 3);
fail_unless(document->getVersion() == 1);
fail_unless(document->getPlugin("fbc") != NULL);
fail_unless(document->getPlugin("fbc")->getPackageVersion() == 2);
}
// ensure that all the v1 stuff is no longer there
FbcModelPlugin* mplug = dynamic_cast<FbcModelPlugin*>(
document->getModel()->getPlugin("fbc"));
fail_unless(mplug != NULL);
fail_unless(mplug->isSetStrict());
fail_unless(mplug->getNumGeneAssociations() == 0);
fail_unless(mplug->getNumFluxBounds() == 0);
delete document;
}
END_TEST
START_TEST (test_FbcExtension_read_L3V1V1_defaultNS)
{
char *filename = safe_strcat(TestDataDirectory, "fbc_example1_defaultNS.xml");
SBMLDocument *document = readSBMLFromFile(filename);
fail_unless(document->getPackageName() == "core");
Model *model = document->getModel();
fail_unless(model != NULL);
fail_unless(model->getPackageName() == "core");
fail_unless(document->getNumErrors() == 0);
// get the fbc plugin
FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
fail_unless(mplugin != NULL);
fail_unless(mplugin->getNumObjectives() == 1);
fail_unless(mplugin->getListOfObjectives()->getPackageName() == "fbc");
Objective* objective = mplugin->getObjective(0);
fail_unless(objective->getId() == "obj1");
fail_unless(objective->getType() == "maximize");
fail_unless(objective->getNumFluxObjectives() == 1);
fail_unless(objective->getPackageName() == "fbc");
fail_unless(objective->getListOfFluxObjectives()->getPackageName() == "fbc");
FluxObjective* fluxObjective = objective->getFluxObjective(0);
fail_unless(fluxObjective->getReaction() == "J8");
fail_unless(fluxObjective->getPackageName() == "fbc");
fail_unless(fluxObjective->getCoefficient() == 1);
fail_unless(mplugin->getNumFluxBounds() == 1);
fail_unless(mplugin->getListOfFluxBounds()->getPackageName() == "fbc");
FluxBound* bound = mplugin->getFluxBound(0);
fail_unless(bound->getId() == "bound1");
fail_unless(bound->getPackageName() == "fbc");
fail_unless(bound->getReaction() == "J0");
fail_unless(bound->getOperation() == "equal");
fail_unless(bound->getValue() == 10);
delete document;
}
int
FbcToCobraConverter::convert()
{
int result = LIBSBML_OPERATION_FAILED;
if (mDocument == NULL)
{
return LIBSBML_INVALID_OBJECT;
}
Model* mModel = mDocument->getModel();
if (mModel == NULL)
{
return LIBSBML_INVALID_OBJECT;
}
FbcModelPlugin *plugin =
static_cast<FbcModelPlugin*>(mDocument->getModel()->getPlugin("fbc"));
// if we have don't have a fbc model we cannot do the conversion
if (plugin == NULL || mDocument->getLevel() != 3)
{
return LIBSBML_OPERATION_FAILED;
}
// collect information
Model* model = mDocument->getModel();
map<const string, int> chargeMap;
map<const string, string> formulaMap;
for (unsigned int i = 0; i < model->getNumSpecies(); ++i)
{
Species* current = model->getSpecies(i);
const string& currentId = current->getId();
FbcSpeciesPlugin *splugin = static_cast<FbcSpeciesPlugin*>(current->getPlugin("fbc"));
if (splugin == NULL)
continue;
if (splugin->isSetCharge())
{
chargeMap[currentId] = splugin->getCharge();
}
if (splugin->isSetChemicalFormula())
{
formulaMap[currentId] = splugin->getChemicalFormula();
}
}
// create KineticLaw
for (unsigned int i = 0; i < model->getNumReactions(); ++i)
{
Reaction* reaction = model->getReaction(i);
if (reaction == NULL)
continue;
createKineticLawForReaction(reaction);
}
// update kinetic law from bounds
for (unsigned int i = 0; i < plugin->getNumFluxBounds(); ++i)
{
FluxBound *current = plugin->getFluxBound(i);
if (current == NULL)
continue;
Reaction* reaction = model->getReaction(current->getReaction());
if (reaction == NULL)
continue;
updateKineticLawFromBound(reaction, current);
}
setObjectiveCoefficient(plugin, model);
// disable package
mDocument->enablePackage("http://www.sbml.org/sbml/level3/version1/fbc/version1", "fbc",false);
// convert model to L2V1 (as L2V2 is the last model that had charge)
mDocument->setConversionValidators(AllChecksON & UnitsCheckOFF);
ConversionProperties prop(new SBMLNamespaces(2,1));
prop.addOption("strict", false, "should validity be preserved");
prop.addOption("ignorePackages", true, "convert even if packages are used");
prop.addOption("setLevelAndVersion", true, "convert the document to the given level and version");
int conversionResult = mDocument->convert(prop);
if (conversionResult != LIBSBML_OPERATION_SUCCESS)
return conversionResult;
// set charge on species
for (unsigned int i = 0; i < model->getNumSpecies(); ++i)
{
Species* current = model->getSpecies(i);
const string currentId = current->getId();
int charge = chargeMap[currentId];
if (charge != 0)
current->setCharge(charge);
const string formula = formulaMap[currentId];
if (!formula.empty())
{
current->setNotes( getNotesForFormula(formula) );
}
}
result = LIBSBML_OPERATION_SUCCESS;
return result;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
SBMLNamespaces sbmlns(3,1,"fbc",1);
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
document->setPackageRequired("fbc", 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->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node2");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node3");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node4");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node5");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node6");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node7");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node8");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node0");
species->setCompartment("compartment");
species->setBoundaryCondition(true);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node9");
species->setCompartment("compartment");
species->setBoundaryCondition(true);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
Reaction* reaction = model->createReaction();
reaction->setId("J0");
reaction->setReversible(false);
reaction->setFast(false);
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("Node0");
reactant->setStoichiometry(1);
reactant->setConstant(true);
SpeciesReference* product = reaction->createProduct();
product->setSpecies("Node1");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J1");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node1");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node2");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J2");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node2");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node3");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J3");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node1");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node4");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J4");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node4");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node3");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J5");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node3");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node5");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J6");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node5");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node6");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J7");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node6");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node7");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J8");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node5");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node8");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J9");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node8");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node7");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J10");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node7");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node9");
product->setStoichiometry(1);
product->setConstant(true);
//
// Get a FbcModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be casted for the
// corresponding derived class.
//
FbcModelPlugin* mplugin
= static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
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");
// mark obj1 as active objective
mplugin->setActiveObjectiveId("obj1");
FluxObjective* fluxObjective = objective->createFluxObjective();
fluxObjective->setReaction("J8");
fluxObjective->setCoefficient(1);
writeSBML(document,"fbc_example1.xml");
delete document;
}
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_FbcExtension_create_and_write_L3V1V1)
{
FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 1);
// create the document
SBMLDocument *document = new SBMLDocument(sbmlns);
delete sbmlns;
// 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);
string s1 = writeSBMLToStdString(document);
// check clone()
SBMLDocument* document2 = document->clone();
string s2 = writeSBMLToStdString(document2);
fail_unless(s1 == s2);
// check operator=
Model m = *(document->getModel());
document2->setModel(&m);
s2 = writeSBMLToStdString(document2);
fail_unless(s1 == s2);
delete document2;
delete document;
}
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;
}
END_TEST
START_TEST(test_FbcExtension_parseGeneAssociation)
{
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/version1' level='3' version='1' fbc:required='false'>"
" <model id='M' name='E' timeUnits='dimensionless'>"
" <annotation>"
" <listOfGeneAssociations xmlns='http://www.sbml.org/sbml/level3/version1/fbc/version1'>"
" <geneAssociation id='ga_1' reaction='R_2DGLCNRx'>"
" <gene reference='B3553'/>"
" </geneAssociation>"
" </listOfGeneAssociations>"
" </annotation>"
" </model>"
"</sbml>"
;
const char* model2 =
"<?xml version='1.0' encoding='UTF-8'?>"
"<sbml xmlns='http://www.sbml.org/sbml/level3/version1/core' xmlns:fbc='http://www.sbml.org/sbml/level3/version1/fbc/version1' metaid='_1f29713d_1639_4193_9935_d6c7ec5255c6' level='3' version='1' fbc:required='false'>"
" <model metaid='meta' id='id' name='name' timeUnits='dimensionless'>"
" <notes>"
" <p xmlns='http://www.w3.org/1999/xhtml'>"
" I prevent you from reading annotations ... "
" </p>"
" </notes>"
" <annotation>"
" <listOfGeneAssociations xmlns='http://www.sbml.org/sbml/level3/version1/fbc/version1'>"
" <geneAssociation id='ga_1' reaction='MNXR2184_i'>"
" <or>"
" <gene reference='MCON_1478_I'/>"
" <gene reference='MCON_2528_I'/>"
" <gene reference='MCON_3321_I'/>"
" <gene reference='METACYC_GHHN_1245_MONOMER_I'/>"
" <gene reference='METACYC_GHHN_2657_MONOMER_I'/>"
" <gene reference='METACYC_GHHN_2722_MONOMER_I'/>"
" </or>"
" </geneAssociation>"
" </listOfGeneAssociations>"
" </annotation>"
" </model>"
"</sbml>"
;
const char* model3 =
"<?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/version1' level='3' version='1' fbc:required='false'>"
" <model id='M' name='E' timeUnits='dimensionless'>"
" <annotation>"
" <listOfGeneAssociations xmlns='http://www.sbml.org/sbml/level3/version1/fbc/version1'>"
" <geneAssociation id='ga_1' reaction='R_2DGLCNRx'>"
" <gene reference='B3553.FR1.F121312'/>"
" </geneAssociation>"
" </listOfGeneAssociations>"
" </annotation>"
" </model>"
"</sbml>"
;
const char* model4 =
"<?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/version1' level='3' version='1' fbc:required='false'>"
" <model id='M' name='E' timeUnits='dimensionless'>"
" <annotation>"
" <listOfGeneAssociations xmlns='http://www.sbml.org/sbml/level3/version1/fbc/version1'>"
" <geneAssociation id='ga_1' reaction='R_2DGLCNRx'>"
" <gene reference='3.14'/>"
" </geneAssociation>"
" </listOfGeneAssociations>"
" </annotation>"
" </model>"
"</sbml>"
;
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->getNumGeneAssociations() == 1);
SBMLDocument_free(doc);
doc = readSBMLFromString(model2);
fail_unless(doc->getModel() != NULL);
fbc = dynamic_cast<FbcModelPlugin*>(doc->getModel()->getPlugin("fbc"));
fail_unless(fbc != NULL);
fail_unless(fbc->getNumGeneAssociations() == 1);
SBMLDocument_free(doc);
doc = readSBMLFromString(model3);
fail_unless(doc->getModel() != NULL);
fbc = dynamic_cast<FbcModelPlugin*>(doc->getModel()->getPlugin("fbc"));
fail_unless(fbc != NULL);
fail_unless(fbc->getNumGeneAssociations() == 1);
SBMLDocument_free(doc);
doc = readSBMLFromString(model4);
fail_unless(doc->getModel() != NULL);
fbc = dynamic_cast<FbcModelPlugin*>(doc->getModel()->getPlugin("fbc"));
fail_unless(fbc != NULL);
fail_unless(fbc->getNumGeneAssociations() == 1);
SBMLDocument_free(doc);
Association* test = Association::parseInfixAssociation("F1.F2.F3 OR F2.f3.f4");
fail_unless(test != NULL);
fail_unless(test->toInfix() == "(F1.F2.F3 or F2.f3.f4)");
test = Association::parseInfixAssociation("3.1 or 3.2");
fail_unless(test != NULL);
fail_unless(test->toInfix() == "(3.1 or 3.2)");
}
Model* CompModelPlugin::flattenModel() const
{
//First make a copy of our parent (the model to be flattened):
const Model* parent = static_cast<const Model*>(getParentSBMLObject());
if (parent==NULL) {
return NULL;
}
//doc needs to be non-const so that the error messages can be updated. Otherwise, nothing changes.
SBMLDocument* doc = const_cast<SBMLDocument*>(getSBMLDocument());
if (doc==NULL) {
return NULL;
}
//Set the original document so that it can find the model definitions
//and external model definitions while we flatten.
Model* flat = parent->clone();
flat->setSBMLDocument(doc);
CompModelPlugin* flatplug =
static_cast<CompModelPlugin*>(flat->getPlugin(getPrefix()));
// Now instantiate its submodels and
// follow all renaming/deletion/replacement rules.
vector<const Model*> submods;
int success = flatplug->instantiateSubmodels();
if (success != LIBSBML_OPERATION_SUCCESS) {
//instantiateSubmodels sets its own error messages.
delete flat;
return NULL;
}
//Now start the aggregation process.
//This goes from the bottom up, calling 'appendFrom' iteratively
//(from the plugin).
for (unsigned int sm=0; sm<flatplug->getNumSubmodels(); sm++)
{
Model* submodel = flatplug->getSubmodel(sm)->getInstantiation();
if (submodel==NULL) {
//getInstantiation should be calling a cached value by now, but if not, it will set its own error messages.
delete flat;
return NULL;
}
CompModelPlugin* submodplug =
static_cast<CompModelPlugin*>(submodel->getPlugin(getPrefix()));
if (submodplug != NULL) {
//Strip the ports from the submodel, as we no longer need them.
while (submodplug->getNumPorts() > 0)
{
delete submodplug->removePort(0);
}
}
success = flat->appendFrom(submodel);
if (success != LIBSBML_OPERATION_SUCCESS) {
string error = "Unable to flatten model in CompModelPlugin::flattenModel: appending elements from the submodel '" + submodel->getId() + "' to the elements of the parent model failed.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
delete flat;
return NULL;
}
#ifdef LIBSBML_HAS_PACKAGE_FBC
// for an fbc v2 model we need to check that the model element
// in the flat document has the fbc:strict attribute
// note this can happen if the parent document did not have fbc but
// included a submodel from an external document that did
if (SBMLExtensionRegistry::isPackageEnabled("fbc"))
{
FbcModelPlugin *mplugin = static_cast<FbcModelPlugin*>
(flat->getPlugin("fbc"));
if (mplugin != NULL && mplugin->getPackageVersion() == 2
&& mplugin->isSetStrict() == false)
{
mplugin->setStrict(false);
}
}
#endif // LIBSBML_HAS_PACKAGE_FBC
}
// Now we clear the saved referenced elements in the local Port objects,
// but point them to the new object if necessary.
flatplug->resetPorts();
// Next, strip the package info from 'flat'.
// We're going to remove everything but the Ports:
flatplug->mListOfSubmodels.clear();
flatplug->clearReplacedElements();
flatplug->unsetReplacedBy();
List* allelements = flat->getAllElements();
vector<SBase*> nonReplacedElements;
for (unsigned int el=0; el<allelements->getSize(); el++)
{
SBase* element = static_cast<SBase*>(allelements->get(el));
int type = element->getTypeCode();
if (!(type==SBML_COMP_REPLACEDBY ||
type==SBML_COMP_REPLACEDELEMENT ||
type==SBML_COMP_SBASEREF))
{
nonReplacedElements.push_back(element);
}
}
// delete the list
delete allelements;
for (unsigned int el=0; el<nonReplacedElements.size(); el++)
{
SBase* element = nonReplacedElements[el];
CompSBasePlugin* elplug =
static_cast<CompSBasePlugin*>(element->getPlugin(getPrefix()));
if (elplug != NULL)
{
elplug->clearReplacedElements();
elplug->unsetReplacedBy();
}
}
//Finally, unset the document again.
flat->setSBMLDocument(NULL);
return flat;
}
