C++ (Cpp) QualModelPlugin::createQualitativeSpecies Examples

Example #1

File: qual_example1.cpp Project: sys-bio/libroadrunner-deps

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;
}

Example #2

File: TestWriteQualExtension.cpp Project: 0u812/roadrunner-backup

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;  
}