/// <summary>
/// Converts a SBML UnitDefinition into a MoBi Unit.
/// </summary>
public IDimension ConvertUnit(UnitDefinition unitDefinition)
{
var sbmlUnit = unitDefinition.getId();
var dimension = _moBiDimensionFactory.TryGetDimensionCaseInsensitive(sbmlUnit);
if (dimension != Constants.Dimension.NO_DIMENSION)
{
_sbmlInformation.MobiDimension[sbmlUnit] = dimension;
return(dimension);
}
var newFactor = 1.0;
var unitsList = new List <Unit>();
var brList = new List <BaseDimensionRepresentation>();
for (long i = 0; i < unitDefinition.getNumUnits(); i++)
{
var mobiUnit = SBMLBaseUnitToMoBi(unitDefinition.getUnit(i));
if (mobiUnit == null)
{
continue;
}
var unitDimension = _moBiDimensionFactory.DimensionForUnit(mobiUnit.Name);
var unitBr = unitDimension.BaseRepresentation;
unitBr = SetExponents(unitDefinition, unitBr, i);
brList.Add(unitBr);
if (Math.Abs(newFactor) < 0.0001)
{
newFactor = unitDefinition.getUnit(i).getMultiplier() * Math.Pow(10, unitDefinition.getUnit(i).getScale()) * Math.Pow(mobiUnit.Factor, unitDefinition.getUnit(i).getExponent());
}
else
{
newFactor = newFactor * unitDefinition.getUnit(i).getMultiplier() * Math.Pow(10, unitDefinition.getUnit(i).getScale()) * Math.Pow(mobiUnit.Factor, unitDefinition.getUnit(i).getExponent());
}
unitsList.Add(mobiUnit);
}
var baseDimensionRepresentation = CreateBaseDimRepresentationExponents(brList);
IDimension newDim = new Dimension(baseDimensionRepresentation, String.Format("SBML_{0}", unitDefinition.getId()), String.Format("SBML_{0}_BaseUnit", unitDefinition.getId()));
var newBaseUnit = newDim.BaseUnit;
newBaseUnit.Visible = false;
var newUnit = new Unit(unitDefinition.getId(), newFactor, 0);
newDim.AddUnit(newUnit);
newDim.DefaultUnit = newUnit;
_sbmlInformation.MobiDimension[sbmlUnit] = newDim;
if (_moBiDimensionFactory.Dimensions.All(dim => dim.Name != newDim.Name))
{
_moBiDimensionFactory.AddDimension(newDim);
}
return(newDim);
}
public void test_UnitDefinition_createUnit()
{
UnitDefinition m = new UnitDefinition(2, 2);
Unit p = m.createUnit();
assertTrue(m.getNumUnits() == 1);
assertTrue((p).getLevel() == 2);
assertTrue((p).getVersion() == 2);
m = null;
}
public void test_UnitDefinition_addUnit4()
{
UnitDefinition m = new UnitDefinition(2, 2);
Unit p = null;
int i = m.addUnit(p);
assertTrue(i == libsbml.LIBSBML_OPERATION_FAILED);
assertTrue(m.getNumUnits() == 0);
m = null;
}
public void test_Model_createUnit()
{
Model m = new Model(2, 2);
UnitDefinition p = m.createUnitDefinition();
Unit u = m.createUnit();
assertTrue(p.getNumUnits() == 1);
assertTrue((u).getLevel() == 2);
assertTrue((u).getVersion() == 2);
m = null;
}
public void test_Unit_parent_create()
{
UnitDefinition ud = new UnitDefinition(2, 4);
Unit u = ud.createUnit();
assertTrue(ud.getNumUnits() == 1);
ListOf lo = ud.getListOfUnits();
assertTrue(lo == ud.getUnit(0).getParentSBMLObject());
assertTrue(lo == u.getParentSBMLObject());
assertTrue(ud == lo.getParentSBMLObject());
ud = null;
}
public void test_UnitDefinition_addUnit3()
{
UnitDefinition m = new UnitDefinition(2, 2);
Unit p = new Unit(1, 2);
p.setKind(libsbml.UNIT_KIND_MOLE);
int i = m.addUnit(p);
assertTrue(i == libsbml.LIBSBML_LEVEL_MISMATCH);
assertTrue(m.getNumUnits() == 0);
p = null;
m = null;
}
public void test_UnitDefinition_addUnit1()
{
UnitDefinition m = new UnitDefinition(2, 2);
Unit p = new Unit(2, 2);
int i = m.addUnit(p);
assertTrue(i == libsbml.LIBSBML_INVALID_OBJECT);
p.setKind(libsbml.UNIT_KIND_MOLE);
i = m.addUnit(p);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(m.getNumUnits() == 1);
p = null;
m = null;
}
public void test_UnitDefinition_addUnit()
{
Unit u = new Unit(2, 4);
u.setKind(libsbml.UNIT_KIND_MOLE);
UD.addUnit(u);
assertTrue(UD.getNumUnits() == 1);
u = null;
}
public void test_Unit_parent_add()
{
UnitDefinition ud = new UnitDefinition(2, 4);
Unit u = new Unit(2, 4);
u.setKind(libsbml.UNIT_KIND_MOLE);
ud.addUnit(u);
u = null;
assertTrue(ud.getNumUnits() == 1);
ListOf lo = ud.getListOfUnits();
assertTrue(lo == ud.getUnit(0).getParentSBMLObject());
assertTrue(ud == lo.getParentSBMLObject());
ud = null;
}
public void test_UnitDefinition_createWithName()
{
UnitDefinition ud = new UnitDefinition(2, 4);
ud.setName("mmol_per_liter_per_sec");
assertTrue(ud.getTypeCode() == libsbml.SBML_UNIT_DEFINITION);
assertTrue(ud.getMetaId() == "");
assertTrue(ud.getNotes() == null);
assertTrue(ud.getAnnotation() == null);
assertTrue(ud.getId() == "");
assertTrue(("mmol_per_liter_per_sec" == ud.getName()));
assertEquals(true, ud.isSetName());
assertTrue(ud.getNumUnits() == 0);
ud = null;
}
public void test_SBMLConvert_convertToL3_defaultUnits()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
c.setId(sid);
c.setSize(1.2);
c.setUnits("volume");
assertTrue(m.getNumUnitDefinitions() == 0);
assertTrue(d.setLevelAndVersion(3, 1, true) == true);
assertTrue(m.getNumUnitDefinitions() == 2);
UnitDefinition ud = m.getUnitDefinition(0);
assertTrue(ud != null);
assertTrue(("volume" == ud.getId()));
assertTrue(ud.getNumUnits() == 1);
Unit u = ud.getUnit(0);
assertTrue(u.getKind() == libsbml.UNIT_KIND_LITRE);
assertTrue(u.getExponent() == 1);
assertTrue(u.getMultiplier() == 1);
assertTrue(u.getScale() == 0);
ud = m.getUnitDefinition(1);
assertTrue(ud != null);
assertTrue(("area" == ud.getId()));
assertTrue(ud.getNumUnits() == 1);
u = ud.getUnit(0);
assertTrue(u.getKind() == libsbml.UNIT_KIND_METRE);
assertTrue(u.getExponent() == 2);
assertTrue(u.getMultiplier() == 1);
assertTrue(u.getScale() == 0);
assertTrue(("second" == m.getTimeUnits()));
d = null;
}
public void test_Unit_ancestor_add()
{
UnitDefinition ud = new UnitDefinition(2, 4);
Unit u = new Unit(2, 4);
u.setKind(libsbml.UNIT_KIND_MOLE);
ud.addUnit(u);
u = null;
assertTrue(ud.getNumUnits() == 1);
ListOf lo = ud.getListOfUnits();
Unit obj = ud.getUnit(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_UNIT_DEFINITION) == ud);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
ud = null;
}
public void test_Unit_ancestor_create()
{
UnitDefinition ud = new UnitDefinition(2, 4);
Unit u = ud.createUnit();
assertTrue(ud.getNumUnits() == 1);
ListOf lo = ud.getListOfUnits();
assertTrue(u.getAncestorOfType(libsbml.SBML_UNIT_DEFINITION) == ud);
assertTrue(u.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(u.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(u.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
Unit obj = ud.getUnit(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_UNIT_DEFINITION) == ud);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
ud = null;
}
