C++ (Cpp) UnitDefinition::getNumUnits Examples

Example #1

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

END_TEST

START_TEST (test_DerivedUnitDefinition_parameter)
{
  UnitDefinition *fud = m->getParameter(0)->getDerivedUnitDefinition();

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

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

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

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

  fud = m->getParameter(1)->getDerivedUnitDefinition();

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

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

}

Example #2

File: TestCalculatedUnitDefinitions.cpp Project: 0u812/libsbml.js.frozen

END_TEST


START_TEST (test_CalcUnitDefinition_assignmentRule1)
{
  UnitDefinition *fud = m->getParameter("e")->getDerivedUnitDefinition();

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

  m->getParameter("e")->setCalculatingUnits(true);
  fud = m->getParameter("e")->getDerivedUnitDefinition();
  m->getParameter("e")->setCalculatingUnits(false);

  fail_unless(fud->getNumUnits() == 2);
  fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);

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

  fail_unless(fud->getUnit(1)->getMultiplier() == 1);
  fail_unless(fud->getUnit(1)->getScale() == 0);
  fail_unless(fud->getUnit(1)->getExponent() == -1);
  fail_unless(fud->getUnit(1)->getOffset() == 0.0);
  fail_unless(fud->getUnit(1)->getKind() == UNIT_KIND_SECOND);
  delete fud;
}

Example #3

File: TestCalculatedUnitDefinitions.cpp Project: 0u812/libsbml.js.frozen

END_TEST


START_TEST (test_CalcUnitDefinition_local1)
{
  UnitDefinition *fud = m->getReaction("R5")->getKineticLaw()
    ->getLocalParameter(0)->getDerivedUnitDefinition();

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

  m->getReaction("R5")->getKineticLaw()
    ->getLocalParameter(0)->setCalculatingUnits(true);
  fud = m->getReaction("R5")->getKineticLaw()
    ->getLocalParameter(0)->getDerivedUnitDefinition();
  m->getReaction("R5")->getKineticLaw()
    ->getLocalParameter(0)->setCalculatingUnits(false);

  fail_unless(fud->getNumUnits() == 1);
  fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);

  fail_unless(fud->getUnit(0)->getMultiplier() == 1);
  fail_unless(fud->getUnit(0)->getScale() == 0);
  fail_unless(fud->getUnit(0)->getExponent() == 1);
  fail_unless(fud->getUnit(0)->getOffset() == 0.0);
  fail_unless(fud->getUnit(0)->getKind() == UNIT_KIND_SECOND);
}

Example #4

File: TestUnitFormulaFormatter1.cpp Project: mgaldzic/copasi_api

END_TEST

START_TEST (test_UnitFormulaFormatter1_getUnitDefinition_function)
{
    UnitDefinition * ud;

    /* function applied to numbers only */
    ud = uff->getUnitDefinition(m->getRule(0)->getMath());

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

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


    /* function applied to components */
    uff->resetFlags();
    ud = uff->getUnitDefinition(m->getRule(1)->getMath());

    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_METRE);

    /* function with two arguments but only one bvar */
    uff->resetFlags();
    ud = uff->getUnitDefinition(m->getRule(2)->getMath());

    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() == 3);
    fail_unless(ud->getUnit(0)->getOffset() == 0.0);
    fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);

    /* function with two arguments but only one bvar */
    uff->resetFlags();
    ud = uff->getUnitDefinition(m->getRule(3)->getMath());

    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_SECOND);

    delete ud;

}

Example #5

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

END_TEST

START_TEST (test_DerivedUnitDefinition_species)
{
  UnitDefinition *fud = m->getSpecies(0)->getDerivedUnitDefinition();

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

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

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

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

  fud = m->getSpecies(1)->getDerivedUnitDefinition();

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

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

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

  fud = m->getSpecies(2)->getDerivedUnitDefinition();

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

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

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

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

}

Example #6

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

END_TEST

START_TEST (test_DerivedUnitDefinition_rule)
{
  UnitDefinition *fud = m->getRule(0)->getDerivedUnitDefinition();
  bool undecl = m->getRule(0)->containsUndeclaredUnits();

  fail_unless(undecl == 1);

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

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


  fud = m->getRule(1)->getDerivedUnitDefinition();
  undecl = m->getRule(1)->containsUndeclaredUnits();

  fail_unless(undecl == 1);

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

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

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

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

  fud = m->getRule(2)->getDerivedUnitDefinition();
  undecl = m->getRule(2)->containsUndeclaredUnits();

  fail_unless(undecl == 1);

  fail_unless(fud->getNumUnits() == 1);
  
  fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);

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

Example #7

File: TestUnitFormulaFormatter.cpp Project: mgaldzic/copasi_api

END_TEST

START_TEST (test_UnitFormulaFormatter_getUnitDefinition_times)
{
  UnitDefinition * ud = new UnitDefinition(2, 4);

  ud = uff->getUnitDefinition(m->getRule(5)->getMath());

  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() == 2);
  fail_unless(ud->getUnit(0)->getOffset() == 0.0);
  fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);

  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_SECOND);

  ud = uff->getUnitDefinition(m->getRule(9)->getMath());

  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_METRE);

  /* check an invalid node */
  delete ud;
  UnitDefinition * ud1 = new UnitDefinition(m->getLevel(), m->getVersion());
  ASTNode *node = new ASTNode(AST_TIMES);
  
  ud1 = uff->getUnitDefinition(node);

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

  delete ud1;
  delete node;

}

Example #8

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

END_TEST



START_TEST(test_unitdefinition_divide2)
{
  UnitDefinition* ud = new UnitDefinition(2, 2);
  UnitDefinition* ud1 = new UnitDefinition(2, 2);
  UnitDefinition* udTemp;

  Unit* u  = ud->createUnit();
  u->setKind(UNIT_KIND_METRE);
  Unit* u1 = ud1->createUnit();
  u1->setKind(UNIT_KIND_MOLE);
  
  udTemp = UnitDefinition::divide(ud, ud1);

  fail_unless(udTemp->getNumUnits() == 2);
  fail_unless(udTemp->getUnit(0)->getKind() == UNIT_KIND_METRE);
  fail_unless(udTemp->getUnit(1)->getKind() == UNIT_KIND_MOLE);
  fail_unless(udTemp->getUnit(1)->getExponent() == -1);
  fail_unless(udTemp->getLevel() == 2);
  fail_unless(udTemp->getVersion() == 2);

  delete ud1;
  delete ud;
  delete udTemp;
 }

Example #9

File: ArgumentsUnitsCheckWarnings.cpp Project: mgaldzic/copasi_api

/**
  * Checks that the units of the arguments 
  * of the function are dimensionless
  * and that there is only one argument
  *
  * If inconsistent units are found, an error message is logged.
  */
void 
ArgumentsUnitsCheckWarnings::checkDimensionlessArgs (const Model& m, 
                                           const ASTNode& node, 
                                           const SBase & sb, 
                                           bool inKL, int reactNo)
{
  /* check that node has children */
  if (node.getNumChildren() == 0)
  {
    return;
  }

  UnitDefinition *dim = new UnitDefinition(m.getSBMLNamespaces());
  Unit *unit = new Unit(m.getSBMLNamespaces());
  unit->setKind(UNIT_KIND_DIMENSIONLESS);
  unit->initDefaults();
  UnitDefinition * tempUD;
  dim->addUnit(unit);
  
  UnitFormulaFormatter *unitFormat = new UnitFormulaFormatter(&m);

  tempUD = unitFormat->getUnitDefinition(node.getChild(0), inKL, reactNo);
  
  if (tempUD->getNumUnits() != 0 && 
    !UnitDefinition::areEquivalent(dim, tempUD)) 
  {
    logInconsistentDimensionless(node, sb);
  }

  delete tempUD;
  delete dim;
  delete unit;
  delete unitFormat;

}

Example #10

File: TestUnitFormulaFormatter.cpp Project: mgaldzic/copasi_api

END_TEST


START_TEST (test_UnitFormulaFormatter_getUnitDefinition_reaction)
{
  UnitDefinition * ud = new UnitDefinition(2, 4);

  ud = uff->getUnitDefinition(m->getRule(13)->getMath());

  fail_unless(ud->getNumUnits() == 3);

  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_METRE);

  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_MOLE);

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

  delete ud;

}

Example #11

File: TestUnitFormulaFormatter3.cpp Project: sys-bio/libroadrunner-deps

END_TEST

#if (0)
START_TEST (test_getUnitDefinition_power_minus_double_exponent)
{
  ASTNode * node = new ASTNode(AST_POWER);
  ASTNode * c = new ASTNode(AST_NAME);
  c->setName("k");
  ASTNode * c1 = new ASTNode(AST_REAL);
  c1->setValue(0.3);
  ASTNode * c2 = new ASTNode(AST_MINUS);
  c2->addChild(c1);
  node->addChild(c);
  node->addChild(c2);

  UnitDefinition * ud = NULL;
    
  ud = uff->getUnitDefinition(node);
  
  fail_unless(uff->getContainsUndeclaredUnits() == false);
  fail_unless(uff->canIgnoreUndeclaredUnits() == false);

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

  fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
  fail_unless(util_isEqual(ud->getUnit(0)->getExponentAsDouble(), -0.3));

  delete node;
  delete ud;

}

Example #12

File: TestUnitFormulaFormatter3.cpp Project: sys-bio/libroadrunner-deps

END_TEST


START_TEST (test_getUnitDefinition_power_three_children)
{
  ASTNode * node = new ASTNode(AST_POWER);
  ASTNode * c = new ASTNode(AST_NAME);
  c->setName("k");
  ASTNode * c1 = new ASTNode(AST_INTEGER);
  c1->setValue(1);
  ASTNode * c2 = new ASTNode(AST_INTEGER);
  c2->setValue(2);
  node->addChild(c);
  node->addChild(c1);
  node->addChild(c2);

  UnitDefinition * ud = NULL;
    
  ud = uff->getUnitDefinition(node);
  
  fail_unless(uff->getContainsUndeclaredUnits() == true);
  fail_unless(uff->canIgnoreUndeclaredUnits() == false);

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

  delete node;
  delete ud;

}

Example #13

File: TestUnitFormulaFormatter3.cpp Project: sys-bio/libroadrunner-deps

END_TEST
#endif

START_TEST (test_getUnitDefinition_power_dim_param_exponent)
{
  ASTNode * node = new ASTNode(AST_POWER);
  ASTNode * c = new ASTNode(AST_NAME);
  c->setName("k");
  ASTNode * c1 = new ASTNode(AST_NAME);
  c1->setName("a");
  node->addChild(c);
  node->addChild(c1);

  UnitDefinition * ud = NULL;
    
  ud = uff->getUnitDefinition(node);
  
  fail_unless(uff->getContainsUndeclaredUnits() == false);
  fail_unless(uff->canIgnoreUndeclaredUnits() == false);

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

  fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
  fail_unless(util_isEqual(ud->getUnit(0)->getExponentAsDouble(), 3.5));

  delete node;
  delete ud;

}

Example #14

File: TestUnitFormulaFormatter2.cpp Project: sys-bio/libroadrunner-deps

END_TEST


START_TEST (test_UnitFormulaFormatter2_getUnitDefinition_model_extent)
{
  UnitDefinition * ud = NULL;

  /* model extent units */
  ud = uff->getExtentUnitDefinition();

  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;
  
  m->unsetExtentUnits();

  ud1 = uff->getExtentUnitDefinition();

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

  delete ud1;

}

Example #15

File: TestUnitFormulaFormatter3.cpp Project: sys-bio/libroadrunner-deps

END_TEST


START_TEST (test_getUnitDefinition_power_one_child)
{
  ASTNode * node = new ASTNode(AST_POWER);
  ASTNode * c = new ASTNode(AST_NAME);
  c->setName("k");
  node->addChild(c);

  UnitDefinition * ud = NULL;
    
  ud = uff->getUnitDefinition(node);
  
  fail_unless(uff->getContainsUndeclaredUnits() == true);
  fail_unless(uff->canIgnoreUndeclaredUnits() == false);

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

  fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
  fail_unless(util_isEqual(ud->getUnit(0)->getExponent(), 1));


  delete node;
  delete ud;

}

Example #16

File: UnitConversionFactory.cpp Project: jonasfoe/COPASI

/*
 * Eliminate all dimensionless units from the given UnitDefinition.
 * A new UnitDefinition without the dimensionless units is returned.
 * The scale and multiplier are preserved. If the UnitDefinition has only
 * one unit the is a dimensionless, it is not deleted.
 * @param UnitDefinition* pUdef
 * @return UnitDefinition* result
 */
LIBSBML_EXTERN
UnitDefinition* UnitConversionFactory::eliminateDimensionless(UnitDefinition* pUdef)
{
    unsigned int maxUnits = pUdef->getNumUnits();
    UnitDefinition* pTmpUdef = NULL;
    Unit* pU = NULL;

    if (maxUnits > 1)
    {
        int scale = 0;
        double multiplier = 1.0;
        unsigned int i = 0;
        pTmpUdef = new UnitDefinition(UnitConversionFactory::SBML_LEVEL, UnitConversionFactory::SBML_VERSION);

        while (i < maxUnits)
        {
            pU = new Unit(*(pUdef->getUnit(i)));

            if (pU->getKind() != UNIT_KIND_DIMENSIONLESS)
            {
                pTmpUdef->addUnit(pU);
            }
            else
            {
                // conserve scale and multiplier
                scale = scale + pU->getScale();
                multiplier = multiplier * pU->getMultiplier();
            }

            delete pU;
            ++i;
        }

        i = pTmpUdef->getNumUnits();

        if (i > 0 && i < maxUnits)
        {
            pTmpUdef->setName(pUdef->getName());
            pTmpUdef->setId(pUdef->getId());
            pU = pTmpUdef->getUnit(0);
            pU->setScale(pU->getScale() + scale);
            pU->setMultiplier(pU->getMultiplier()*multiplier);
        }
        else
        {
            delete pTmpUdef;
            pTmpUdef = NULL;
        }
    }

    return pTmpUdef;
}

Example #17

File: TestCalculatedUnitDefinitions.cpp Project: 0u812/libsbml.js.frozen

END_TEST


START_TEST (test_CalcUnitDefinition_global_with_local_known)
{
  UnitDefinition *fud = m->getParameter("q")->getDerivedUnitDefinition();

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

  m->getParameter("q")->setCalculatingUnits(true);
  fud = m->getParameter("q")->getDerivedUnitDefinition();
  m->getParameter("q")->setCalculatingUnits(false);

  fail_unless(fud->getNumUnits() == 1);
  fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);

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

Example #18

File: UnitConversionFactory.cpp Project: jonasfoe/COPASI

/*
 * Returns a string representation of the given Unit. THis function is
 * only for debugging purposes.
 * @param const UnitDefinition& uDef
 * @return std::string unitDefinitionRepresentation
 */
LIBSBML_EXTERN
std::string UnitConversionFactory::toString(const UnitDefinition& uDef)
{
    unsigned int maxUnits = uDef.getNumUnits();
    unsigned int i;
    std::stringstream ss;

    for (i = 0; i < maxUnits; ++i)
    {
        ss << "(" << UnitConversionFactory::toString(*(uDef.getUnit(i))) << ") ";
    }

    return ss.str();
}

Example #19

File: Expression2PresentationMMLUnits.cpp Project: mgaldzic/copasi_api

std::string Expression2PresentationMMLUnits::getMathML(const UnitDefinition & ud) const
{
  std::string tmp;

  /*tmp += "<mrow>";
  unsigned int i, imax = ud.getNumUnits();
  for (i=0; i<imax; ++i)
  {
    if (i) tmp += "<mo>&CenterDot;</mo>";
    tmp += getMathML(ud.getUnit(i), false);
  }
  tmp += "</mrow>";*/

  tmp += "<mrow>";
  bool isFirst = true;
  unsigned int i, imax = ud.getNumUnits();

  for (i = 0; i < imax; ++i)
    {
      if (ud.getUnit(i)->getExponent() >= 0)
        {
          if (!isFirst) tmp += "<mo>&CenterDot;</mo>";

          tmp += getMathML(ud.getUnit(i), true);
          isFirst = false;
        }
    }

  if (isFirst) tmp += "<mn>1</mn>"; //there are no units with pos. exponent

  std::string tmp2;
  isFirst = true;

  for (i = 0; i < imax; ++i)
    {
      if (ud.getUnit(i)->getExponent() < 0)
        {
          if (!isFirst) tmp2 += "<mo>&CenterDot;</mo>";

          tmp2 += getMathML(ud.getUnit(i), true);
          isFirst = false;
        }
    }

  if (!isFirst) tmp += "<mo>/</mo>" + tmp2; //only create fraction when there is a denominator

  tmp += "</mrow>";

  return tmp;
}

Example #20

File: TestCalculatedUnitDefinitions.cpp Project: 0u812/libsbml.js.frozen

END_TEST


START_TEST (test_CalcUnitDefinition_global_with_local_unknown)
{
  UnitDefinition *fud = m->getParameter("r")->getDerivedUnitDefinition();

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

  m->getParameter("r")->setCalculatingUnits(true);
  fud = m->getParameter("r")->getDerivedUnitDefinition();
  m->getParameter("r")->setCalculatingUnits(false);

  fail_unless(fud == NULL);
}

Example #21

File: TestCalculatedUnitDefinitions.cpp Project: 0u812/libsbml.js.frozen

END_TEST


START_TEST (test_CalcUnitDefinition_priority)
{
  UnitDefinition *fud = m->getParameter("m")->getDerivedUnitDefinition();

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

  m->getParameter("m")->setCalculatingUnits(true);
  fud = m->getParameter("m")->getDerivedUnitDefinition();
  m->getParameter("m")->setCalculatingUnits(false);

  fail_unless(fud->getNumUnits() == 1);
  fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);

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

  delete fud;
}

Example #22

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

END_TEST

START_TEST (test_DerivedUnitDefinition_reaction)
{
  UnitDefinition *fud = m->getReaction(0)->getKineticLaw()->getDerivedUnitDefinition();
  bool undecl = m->getReaction(0)->getKineticLaw()->containsUndeclaredUnits();

  fail_unless(undecl == 0);

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

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

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

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

  fud = m->getReaction(0)->getReactant(0)->getStoichiometryMath()->getDerivedUnitDefinition();
  undecl = m->getReaction(0)->getReactant(0)->getStoichiometryMath()->containsUndeclaredUnits();

  fail_unless(undecl == 1);

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

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


}

Example #23

File: TestInferUnitsConverter.cpp Project: sn248/Rcppsbml

END_TEST


START_TEST (test_infer_localParam_fromReaction)
{
  string filename(TestDataDirectory);
  filename += "inferUnits-3.xml";

  SBMLDocument* d = readSBMLFromFile(filename.c_str());

  fail_unless(d != NULL);

  LocalParameter * p = d->getModel()->getReaction(1)->
                                 getKineticLaw()->getLocalParameter("k2");

  fail_unless(p->isSetUnits() == false);

  p->setCalculatingUnits(true);
  UnitDefinition *ud = p->getDerivedUnitDefinition();

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


  delete ud;

  // TO DO make the units converter do local parameters;
  //fail_unless(d->getModel()->getNumUnitDefinitions() == 3);
  //
  //SBMLInferUnitsConverter * units = new SBMLInferUnitsConverter();

  //units->setDocument(d);

  //fail_unless (units->convert() == LIBSBML_OPERATION_SUCCESS);

  //kl = d->getModel()->getReaction(1)->getKineticLaw();

  //fail_unless(kl->getLocalParameter("k2")->isSetUnits() == true);
  //fail_unless(kl->getLocalParameter("k2")->getUnits() == "per_time");

  //delete units;
  delete d;
}

Example #24

File: UnitConversionFactory.cpp Project: jonasfoe/COPASI

/*
 * The functions determins wether the given UnitDefinition contains only
 * units from the list given as the second argument.
 * @param const UnitDefinition& uDef
 * @param const ListOf& unitList
 * @return bool containsOnlyGivenUnits
 */
LIBSBML_EXTERN
bool UnitConversionFactory::containsOnlyGivenUnits(const UnitDefinition& uDef, const ListOf& unitList)
{
    bool result = true;
    UnitDefinition* pTmpUdef = UnitConversionFactory::convertToSI(uDef);

    if (pTmpUdef)
    {
        unsigned int i;
        unsigned int maxUnits = pTmpUdef->getNumUnits();

        for (i = 0; i < maxUnits; ++i)
        {
            Unit* pU = pTmpUdef->getUnit(i);
            UnitKind_t kind = pU->getKind();
            unsigned int j;
            unsigned int maxUnits2 = unitList.size();
            bool found = false;

            for (j = 0; j < maxUnits2; ++j)
            {
                const Unit* pU2 = dynamic_cast<const Unit*>(unitList.get(j));

                if (!pU2) break;

                if (pU2->getKind() == kind)
                {
                    found = true;
                    break;
                }
            }

            if (!found)
            {
                result = false;
                break;
            }
        }

        delete pTmpUdef;
    }
    else
    {
        result = false;
    }

    return result;
}

Example #25

File: TestInferUnitsConverter.cpp Project: sn248/Rcppsbml

END_TEST


START_TEST (test_infer_newUD)
{
  string filename(TestDataDirectory);
  filename += "inferUnits.xml";

  SBMLDocument* d = readSBMLFromFile(filename.c_str());

  fail_unless(d != NULL);

  fail_unless(d->getModel()->getParameter("b")->isSetUnits() == false);
  fail_unless(d->getModel()->getNumUnitDefinitions() == 1);

  SBMLInferUnitsConverter * units = new SBMLInferUnitsConverter();

  units->setDocument(d);

  fail_unless (units->convert() == LIBSBML_OPERATION_SUCCESS);

  fail_unless(d->getModel()->getParameter("b")->isSetUnits() == true);
  fail_unless(d->getModel()->getParameter("b")->getUnits() == "unitSid_0");

  fail_unless(d->getModel()->getNumUnitDefinitions() == 2);

  UnitDefinition *ud = d->getModel()->getUnitDefinition(1);

  fail_unless(ud->getId() == "unitSid_0");
  fail_unless(ud->getNumUnits() == 2);
  
  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_LITRE);

  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_METRE);

  delete units;
  delete d;
}

Example #26

File: TestCalculatedUnitDefinitions.cpp Project: 0u812/libsbml.js.frozen

END_TEST


START_TEST (test_CalcUnitDefinition_rateRule_timeUnknown)
{
  m->unsetTimeUnits();

  UnitDefinition *fud = m->getParameter("h")->getDerivedUnitDefinition();

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

  m->getParameter("h")->setCalculatingUnits(true);
  fud = m->getParameter("h")->getDerivedUnitDefinition();
  m->getParameter("h")->setCalculatingUnits(false);

  fail_unless(fud == NULL);
}

Example #27

File: TestCalculatedUnitDefinitions.cpp Project: 0u812/libsbml.js.frozen

END_TEST


START_TEST (test_CalcUnitDefinition_unknownReaction)
{
  m->unsetExtentUnits();

  UnitDefinition *fud = m->getParameter("o")->getDerivedUnitDefinition();

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

  m->getParameter("o")->setCalculatingUnits(true);
  fud = m->getParameter("o")->getDerivedUnitDefinition();
  m->getParameter("o")->setCalculatingUnits(false);

  fail_unless(fud == NULL);
}

Example #28

File: TestSBMLParentObject.cpp Project: alexholehouse/SBMLIntegrator

END_TEST


START_TEST ( test_Unit_parent_create )
{
    UnitDefinition* ud = new UnitDefinition(2, 4);
    Unit * u = ud->createUnit();

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

    ListOf *lo = ud->getListOfUnits();

    fail_unless(lo == ud->getUnit(0)->getParentSBMLObject());
    fail_unless(lo == u->getParentSBMLObject());
    fail_unless(ud == lo->getParentSBMLObject());

    delete ud;
}

Example #29

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

END_TEST

START_TEST (test_DerivedUnitDefinition_initialassignment)
{
  UnitDefinition *fud = m->getInitialAssignment(0)->getDerivedUnitDefinition();
  bool undecl = m->getInitialAssignment(0)->containsUndeclaredUnits();

  fail_unless(undecl == 1);

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

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

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

}

Example #30

File: SbmlReader.cpp Project: csiki/moose-csiki

double SbmlReader::unitsforRates() {
    double lvalue =1;
    for (unsigned int n=0; n < model_->getNumUnitDefinitions(); n++) {
        UnitDefinition * ud = model_->getUnitDefinition(n);
        for (unsigned int ut=0; ut <ud->getNumUnits(); ut++) {
            Unit * unit = ud->getUnit(ut);
            if (ud->getId() == "substance") {
                if ( unit->isMole() ) {
                    double exponent = unit->getExponent();
                    double multiplier = unit->getMultiplier();
                    int scale = unit->getScale();
                    double offset = unit->getOffset();
                    lvalue *= pow( multiplier * pow(10.0,scale), exponent ) + offset;
                    return lvalue;
                }
            }
        }
    }
    return lvalue;
}//unitforRates