LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
if (argc != 2)
{
std::cout << "Usage: example1\n";
return 1;
}
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "qual") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"qual",1,"QUAL");
//
SBMLNamespaces sbmlns(3,1,"qual",1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a qual package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("qual",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(QualExtension::XmlnsL3V1V1,"qual");
//
// (2) Creates a QualPkgNamespaces object (SBMLNamespace derived class for
// qual package. The class is basically used for createing an SBase
// derived objects defined in the qual package) with the given SBML
// level, version, and package version
//
// QualPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// mark qual as required
document->setPackageRequired("qual", true);
// create the Model
Model* model=document->createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("c");
compartment->setConstant(true);
//
// Get a QualModelPlugin 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.
//
QualModelPlugin* mplugin
= static_cast<QualModelPlugin*>(model->getPlugin("qual"));
// create the QualitativeSpecies
QualitativeSpecies* qs = mplugin->createQualitativeSpecies();
qs->setId("s1");
qs->setCompartment("c");
qs->setConstant(false);
qs->setInitialLevel(1);
qs->setMaxLevel(4);
qs->setName("sss");
// create the Transition
Transition* t = mplugin->createTransition();
t->setId("d");
t->setSBOTerm(1);
Input* i = t->createInput();
i->setId("RD");
i->setQualitativeSpecies("s1");
i->setTransitionEffect(INPUT_TRANSITION_EFFECT_NONE);
i->setSign(INPUT_SIGN_NEGATIVE);
i->setThresholdLevel(2);
i->setName("aa");
Output* o = t->createOutput();
o->setId("wd");
o->setQualitativeSpecies("s1");
o->setTransitionEffect(OUTPUT_TRANSITION_EFFECT_PRODUCTION);
o->setOutputLevel(2);
o->setName("aa");
DefaultTerm* dt = t->createDefaultTerm();
dt->setResultLevel(2) ;
FunctionTerm* ft = t->createFunctionTerm();
ASTNode* math = SBML_parseL3Formula("geq(s1, 2)");
ft->setResultLevel(1);
ft->setMath(math);
writeSBML(document,"qual_example1.xml");
delete document;
return 0;
}
END_TEST
START_TEST (test_QualExtension_read_enable_via_sbmldocument_and_write_L3V1V1)
{
const char* s1 =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\">\n"
" <model>\n"
" <listOfCompartments>\n"
" <compartment id=\"c\" constant=\"true\"/>\n"
" </listOfCompartments>\n"
" </model>\n"
"</sbml>\n"
;
const char* s1a =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" xmlns:qual=\"http://www.sbml.org/sbml/level3/version1/qual/version1\" level=\"3\" version=\"1\" qual:required=\"true\">\n"
" <model>\n"
" <listOfCompartments>\n"
" <compartment id=\"c\" constant=\"true\"/>\n"
" </listOfCompartments>\n"
" <qual:listOfQualitativeSpecies>\n"
" <qual:qualitativeSpecies qual:id=\"s1\" qual:compartment=\"c\" qual:constant=\"false\" qual:name=\"sss\" qual:initialLevel=\"1\" qual:maxLevel=\"4\"/>\n"
" </qual:listOfQualitativeSpecies>\n"
" </model>\n"
"</sbml>\n"
;
SBMLDocument *document = readSBMLFromString(s1);
fail_unless(document->getNumPlugins() == 0);
//
// enable the qual package by invoking enablePackage function with SBMLDocument object
//
fail_unless(document->enablePackage(QUAL_XMLNS_L3V1V1, "qual", true) == LIBSBML_OPERATION_SUCCESS);
// mark qual as required
document->setPackageRequired("qual", true);
fail_unless(document->getNumPlugins() == 1);
Model *model = document->getModel();
fail_unless(model != NULL);
fail_unless(model->getNumPlugins() == 1);
//// create the QualitativeSpecies
QualModelPlugin* mplugin = static_cast<QualModelPlugin*>(model->getPlugin("qual"));
fail_unless(mplugin != NULL);
QualitativeSpecies* qs = mplugin->createQualitativeSpecies();
fail_unless(qs->setId("s1") == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setCompartment("c") == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setConstant(false) == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setInitialLevel(1) == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setMaxLevel(4) == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setName("sss") == LIBSBML_OPERATION_SUCCESS);
char *s2 = writeSBMLToString(document);
fail_unless(strcmp(s1a,s2) == 0);
free(s2);
delete document;
}
END_TEST
START_TEST (test_QualExtension_read_L3V1V1_defaultNS)
{
string filename = string(TestDataDirectory) + "qual-example1-defaultNS.xml";
SBMLDocument *document = readSBMLFromFile(filename.c_str());
fail_unless(document->getPackageName() == "core");
Model *model = document->getModel();
fail_unless(model != NULL);
fail_unless(model->getPackageName() == "core");
// get the Qualitative species
QualModelPlugin* mplugin = static_cast<QualModelPlugin*>(model->getPlugin("qual"));
fail_unless(mplugin != NULL);
fail_unless(mplugin->getNumQualitativeSpecies() == 1);
fail_unless(mplugin->getListOfQualitativeSpecies()->getPackageName() == "qual");
fail_unless(mplugin->getNumTransitions() == 1);
fail_unless(mplugin->getListOfTransitions()->getPackageName() == "qual");
QualitativeSpecies* qs = mplugin->getQualitativeSpecies(0);
fail_unless(qs->getPackageName() == "qual");
fail_unless(qs->getId() == "s1");
fail_unless(qs->getName() == "sss");
fail_unless(qs->getMetaId() == "_ddd");
fail_unless(qs->getCompartment() == "c");
fail_unless(qs->getConstant() == false);
fail_unless(qs->getInitialLevel() == 1);
fail_unless(qs->getMaxLevel() == 4);
Transition* t = mplugin->getTransition(0);
fail_unless(t->getPackageName() == "qual");
fail_unless(t->getId() == "d");
fail_unless(t->getNumInputs() == 1);
fail_unless(t->getNumOutputs() == 1);
fail_unless(t->getNumFunctionTerms() == 1);
fail_unless(t->isSetDefaultTerm() == true);
Input *i = t->getInput(0);
fail_unless(i->getPackageName() == "qual");
fail_unless(i->getId() == "RD");
fail_unless(i->getName() == "aa" );
fail_unless(i->getQualitativeSpecies() == "s1");
fail_unless(i->getTransitionEffect() == INPUT_TRANSITION_EFFECT_NONE );
fail_unless(i->getSign() == INPUT_SIGN_NEGATIVE);
fail_unless(i->getThresholdLevel() == 2);
Output *o = t->getOutput(0);
fail_unless(o->getPackageName() == "qual");
fail_unless(o->getId() == "wd");
fail_unless(o->getName() == "asa" );
fail_unless(o->getQualitativeSpecies() == "s1");
fail_unless(o->getTransitionEffect() == OUTPUT_TRANSITION_EFFECT_PRODUCTION );
fail_unless(o->getOutputLevel() == 2);
FunctionTerm* ft1 = t->getFunctionTerm(0);
fail_unless(ft1->getPackageName() == "qual");
fail_unless(ft1->getResultLevel() == 1);
fail_unless(ft1->getMath() != NULL);
DefaultTerm* dt = t->getDefaultTerm();
fail_unless(dt->getPackageName() == "qual");
fail_unless(dt->getResultLevel() == 2);
delete document;
}
END_TEST
START_TEST (test_QualExtension_create_add_and_write_L3V1V1)
{
const char* s1 =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" xmlns:qual=\"http://www.sbml.org/sbml/level3/version1/qual/version1\" level=\"3\" version=\"1\" qual:required=\"true\">\n"
" <model>\n"
" <listOfCompartments>\n"
" <compartment id=\"c\" constant=\"true\"/>\n"
" </listOfCompartments>\n"
" <qual:listOfQualitativeSpecies>\n"
" <qual:qualitativeSpecies metaid=\"ddd\" qual:id=\"s1\" qual:compartment=\"c\" qual:constant=\"false\" qual:name=\"sss\" qual:initialLevel=\"1\" qual:maxLevel=\"4\"/>\n"
" </qual:listOfQualitativeSpecies>\n"
" <qual:listOfTransitions>\n"
" <qual:transition sboTerm=\"SBO:0000001\" qual:id=\"d\">\n"
" <qual:listOfInputs>\n"
" <qual:input qual:id=\"RD\" qual:qualitativeSpecies=\"s1\" qual:transitionEffect=\"none\" qual:name=\"aa\" qual:sign=\"negative\" qual:thresholdLevel=\"2\"/>\n"
" </qual:listOfInputs>\n"
" <qual:listOfOutputs>\n"
" <qual:output qual:id=\"wd\" qual:qualitativeSpecies=\"s1\" qual:transitionEffect=\"production\" qual:name=\"aa\" qual:outputLevel=\"2\"/>\n"
" </qual:listOfOutputs>\n"
" <qual:listOfFunctionTerms>\n"
" <qual:defaultTerm qual:resultLevel=\"1\"/>\n"
" <qual:functionTerm qual:resultLevel=\"2\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <geq/>\n"
" <ci> s1 </ci>\n"
" <cn type=\"integer\"> 2 </cn>\n"
" </apply>\n"
" </math>\n"
" </qual:functionTerm>\n"
" </qual:listOfFunctionTerms>\n"
" </qual:transition>\n"
" </qual:listOfTransitions>\n"
" </model>\n"
"</sbml>\n"
;
QualPkgNamespaces *sbmlns = new QualPkgNamespaces(3,1,1);
// create the document
SBMLDocument *document = new SBMLDocument(sbmlns);
//// mark qual as required
document->setPackageRequired("qual", true);
// create the Model
Model* model= new Model(sbmlns);
// create the Compartment
Compartment* compartment = new Compartment(sbmlns);
compartment->setId("c");
compartment->setConstant(true);
fail_unless(model->addCompartment(compartment) == LIBSBML_OPERATION_SUCCESS);
//// create the QualitativeSpecies
QualModelPlugin* mplugin = static_cast<QualModelPlugin*>(model->getPlugin("qual"));
fail_unless(mplugin != NULL);
QualitativeSpecies* qs = new QualitativeSpecies(sbmlns);
fail_unless(qs->setId("s1") == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setCompartment("c") == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setConstant(false) == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setInitialLevel(1) == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setMaxLevel(4) == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setName("sss") == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setMetaId("ddd") == LIBSBML_OPERATION_SUCCESS);
fail_unless(mplugin->addQualitativeSpecies(qs) == LIBSBML_OPERATION_SUCCESS);
Transition* t = new Transition(sbmlns);
fail_unless(t->setId("d") == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->setSBOTerm(1) == LIBSBML_OPERATION_SUCCESS);
Input* i = new Input(sbmlns);
fail_unless(i->setId("RD") == LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setQualitativeSpecies("s1") == LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setTransitionEffect
(InputTransitionEffect_fromString("none")) == LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setSign(InputSign_fromString("negative"))
== LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setThresholdLevel(2) == LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setName("aa") == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->addInput(i) == LIBSBML_OPERATION_SUCCESS);
Output* o = new Output(sbmlns);
fail_unless(o->setId("wd") == LIBSBML_OPERATION_SUCCESS);
fail_unless(o->setQualitativeSpecies("s1") == LIBSBML_OPERATION_SUCCESS);
fail_unless(o->setTransitionEffect
(OutputTransitionEffect_fromString("production")) == LIBSBML_OPERATION_SUCCESS);
fail_unless(o->setOutputLevel(2) == LIBSBML_OPERATION_SUCCESS);
fail_unless(o->setName("aa") == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->addOutput(o) == LIBSBML_OPERATION_SUCCESS);
FunctionTerm* ft = new FunctionTerm(sbmlns);
ASTNode* math = SBML_parseL3Formula("geq(s1, 2)");
fail_unless(ft->setResultLevel(2) == LIBSBML_OPERATION_SUCCESS);
fail_unless(ft->setMath(math) == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->addFunctionTerm(ft) == LIBSBML_OPERATION_SUCCESS);
DefaultTerm* dt = new DefaultTerm(sbmlns);
fail_unless(dt->setResultLevel(1) == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->setDefaultTerm(dt) == LIBSBML_OPERATION_SUCCESS);
fail_unless(mplugin->addTransition(t) == LIBSBML_OPERATION_SUCCESS);
fail_unless(document->setModel(model) == LIBSBML_OPERATION_SUCCESS);
char *s2 = writeSBMLToString(document);
fail_unless(strcmp(s1,s2) == 0);
free(s2);
delete document;
}
