C++ (Cpp) Species::setUnits Exemples

Exemple #1

Fichier : TestWriteL3SBML.cpp Projet : sn248/Rcppsbml

END_TEST


START_TEST (test_WriteL3SBML_Species)
{
  const char* expected = 
    "<species id=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\""
    " substanceUnits=\"mole\" hasOnlySubstanceUnits=\"false\""
    " boundaryCondition=\"true\" constant=\"true\"/>";


  Species *s = D->createModel()->createSpecies();
  s->setId("Ca2");
  s->setCompartment("cell");
  s->setInitialAmount(0.7);
  s->setUnits("mole");
  s->setBoundaryCondition(true);
  s->setHasOnlySubstanceUnits(false);
  s->setConstant(true);

  char* sbml = s->toSBML();
  fail_unless( equals(expected, sbml) );
  safe_free(sbml);
}

Exemple #2

Fichier : TestUnitFormulaFormatter2.cpp Projet : sys-bio/libroadrunner-deps

END_TEST

START_TEST (test_UnitFormulaFormatter2_getUnitDefinition_species)
{
  UnitDefinition * ud = NULL;
  
  /* species with declared standard units for substance and comp with units*/
  ud = uff->getUnitDefinitionFromSpecies(m->getSpecies(0));

  fail_unless(ud->getNumUnits() == 2);

  fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);

  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_MOLE);

  fail_unless(ud->getUnit(1)->getMultiplier() == 1);
  fail_unless(ud->getUnit(1)->getScale() == 0);
  fail_unless(ud->getUnit(1)->getExponent() == -1);
  fail_unless(ud->getUnit(1)->getOffset() == 0.0);
  fail_unless(ud->getUnit(1)->getKind() == UNIT_KIND_LITRE);

  delete ud;

  ud = uff->getSpeciesSubstanceUnitDefinition(m->getSpecies(0));

  fail_unless(ud->getNumUnits() == 1);

  fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);

  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_MOLE);

  delete ud;

  /* species with declared standard units for substance 
  and hasOnlySubstanceUnits = 1*/
  ud = uff->getUnitDefinitionFromSpecies(m->getSpecies(1));

  fail_unless(ud->getNumUnits() == 1);

  fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);

  fail_unless(ud->getUnit(0)->getMultiplier() == 1);
  fail_unless(ud->getUnit(0)->getScale() == -2);
  fail_unless(ud->getUnit(0)->getExponent() == 1);
  fail_unless(ud->getUnit(0)->getOffset() == 0.0);
  fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);

  delete ud;

  ud = uff->getSpeciesSubstanceUnitDefinition(m->getSpecies(1));

  fail_unless(ud->getNumUnits() == 1);

  fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);

  fail_unless(ud->getUnit(0)->getMultiplier() == 1);
  fail_unless(ud->getUnit(0)->getScale() == -2);
  fail_unless(ud->getUnit(0)->getExponent() == 1);
  fail_unless(ud->getUnit(0)->getOffset() == 0.0);
  fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);

  delete ud;

  /* species with units from model substance*/
  ud = uff->getUnitDefinitionFromSpecies(m->getSpecies(2));

  fail_unless(ud->getNumUnits() == 2);

  fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);

  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_MOLE);

  fail_unless(ud->getUnit(1)->getMultiplier() == 1);
  fail_unless(ud->getUnit(1)->getScale() == 0);
  fail_unless(ud->getUnit(1)->getExponent() == -1);
  fail_unless(ud->getUnit(1)->getOffset() == 0.0);
  fail_unless(ud->getUnit(1)->getKind() == UNIT_KIND_LITRE);

  delete ud;

  ud = uff->getSpeciesSubstanceUnitDefinition(m->getSpecies(2));
 
  fail_unless(ud->getNumUnits() == 1);

  fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);

  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_MOLE);

  delete ud;

  /* species with declared standard units for substance and no spatialSizeUnits*/
  ud = uff->getUnitDefinitionFromSpecies(m->getSpecies(3));

  fail_unless(ud->getNumUnits() == 0);

  delete ud;

  ud = uff->getSpeciesSubstanceUnitDefinition(m->getSpecies(3));
 
  fail_unless(ud->getNumUnits() == 1);
 
  fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);

  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_MOLE);


  ///* check deals with invalid nodes */
  delete ud;
  UnitDefinition * ud1 = NULL;
  
  Species *s = new Species(m->getLevel(), m->getVersion());
  s->setId("s");
  s->setUnits("undefined");

  ud1 = uff->getUnitDefinitionFromSpecies(s);

  fail_unless (ud1->getNumUnits() == 0);

  delete ud1;

  ud1 = uff->getSpeciesSubstanceUnitDefinition(s);

  fail_unless (ud1->getNumUnits() == 0);

  s->setUnits("mole"); // here the compartment size will be NULL

  delete ud1;

  ud1 = uff->getUnitDefinitionFromSpecies(s);

  fail_unless (ud1->getNumUnits() == 1);

  delete ud1;

  ud1 = uff->getSpeciesSubstanceUnitDefinition(s);

  fail_unless (ud1->getNumUnits() == 1);

  delete s;
  delete ud1;

}