/// <summary>
/// The function actually doing the transforming. This function is called
/// once for each SBase element in the model.
/// </summary>
/// <param name="element">the current element</param>
/// <returns>status code</returns>
public override int transform(SBase element)
{
// return in case we don't have a valid element
if (element == null || element.getTypeCode() == libsbml.SBML_LOCAL_PARAMETER)
{
return(libsbml.LIBSBML_OPERATION_SUCCESS);
}
// or if there is nothing to do
if (!element.isSetName() || element.getId() == element.getName())
{
return(libsbml.LIBSBML_OPERATION_SUCCESS);
}
// find the new id
string newId = getValidIdForName(element.getName());
// set it
element.setId(newId);
// remember it
existingIds.Add(newId);
return(libsbml.LIBSBML_OPERATION_SUCCESS);
}
public void test_GetMultipleObjects_noLocalParameters()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == null)
{
;
}
{
}
SBase rxn = d.getElementBySId("J0");
assertTrue(rxn != null);
SBase obj = rxn.getElementBySId("x");
assertTrue(obj == null);
obj = rxn.getElementByMetaId("meta28");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LOCAL_PARAMETER);
d = null;
}
public void test_GetMultipleObjects_noAssignments()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "assignments-invalid.xml";
d = reader.readSBML(filename);
if (d.getModel() == null)
{
;
}
{
}
SBase obj = d.getElementBySId("ia");
assertTrue(obj == null);
obj = d.getElementByMetaId("ia_meta");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_INITIAL_ASSIGNMENT);
obj = d.getElementBySId("ar");
assertTrue(obj == null);
obj = d.getElementByMetaId("ar_meta");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE);
obj = d.getElementBySId("rr");
assertTrue(obj == null);
obj = d.getElementByMetaId("rr_meta");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_RATE_RULE);
obj = d.getElementBySId("ea");
assertTrue(obj == null);
obj = d.getElementByMetaId("ea_meta");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT);
d = null;
}
/**
* Returns a list of all ids from the given list of elements
*/
public static List <string> getAllIds(SBaseList allElements)
{
var result = new List <string>();
if (allElements == null || allElements.getSize() == 0)
{
return(result);
}
for (uint i = 0; i < allElements.getSize(); ++i)
{
SBase current = allElements.get(i);
if (current.isSetId() && current.getTypeCode() != libsbml.SBML_LOCAL_PARAMETER)
{
result.Add(current.getId());
}
}
return(result);
}
public void test_GetMultipleObjects_getId()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == null)
{
;
}
{
}
SBase obj = d.getElementBySId("no_id");
assertTrue(obj == null);
obj = d.getElementBySId("");
assertTrue(obj == null);
obj = d.getElementBySId("find_id");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_MODEL);
obj = d.getElementBySId("func1");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION);
obj = d.getElementBySId("comp");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_COMPARTMENT);
obj = d.getElementBySId("b");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_SPECIES);
obj = d.getElementBySId("x");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_PARAMETER);
obj = d.getElementBySId("J0");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_REACTION);
obj = d.getElementBySId("E0");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_EVENT);
d = null;
}
public void test_GetMultipleObjects_noUnits()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == null)
{
;
}
{
}
SBase obj = d.getElementBySId("volume");
assertTrue(obj == null);
obj = d.getElementByMetaId("meta30");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_UNIT_DEFINITION);
d = null;
}
public void test_GetMultipleObjects_getMetaId()
{
SBMLReader reader = new SBMLReader();
SBMLDocument d;
string filename = "../../sbml/test/test-data/";
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == null)
{
;
}
{
}
SBase obj = d.getElementByMetaId("no_id");
assertTrue(obj == null);
obj = d.getElementByMetaId("");
assertTrue(obj == null);
obj = d.getElementByMetaId("meta1");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_DOCUMENT);
obj = d.getElementByMetaId("meta2");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_MODEL);
obj = d.getElementByMetaId("meta3");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_COMPARTMENT);
obj = d.getElementByMetaId("meta4");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_COMPARTMENT);
obj = d.getElementByMetaId("meta5");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_SPECIES);
obj = d.getElementByMetaId("meta6");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_SPECIES);
obj = d.getElementByMetaId("meta7");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_REACTION);
obj = d.getElementByMetaId("meta8");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_REACTION);
obj = d.getElementByMetaId("meta9");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_SPECIES_REFERENCE);
obj = d.getElementByMetaId("meta10");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE);
obj = d.getElementByMetaId("meta11");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_KINETIC_LAW);
obj = d.getElementByMetaId("meta12");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_EVENT);
obj = d.getElementByMetaId("meta13");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_EVENT);
obj = d.getElementByMetaId("meta14");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_TRIGGER);
obj = d.getElementByMetaId("meta15");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT);
obj = d.getElementByMetaId("meta16");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT);
obj = d.getElementByMetaId("meta17");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_DELAY);
obj = d.getElementByMetaId("meta18");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_PARAMETER);
obj = d.getElementByMetaId("meta19");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_PRIORITY);
obj = d.getElementByMetaId("meta20");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_FUNCTION_DEFINITION);
obj = d.getElementByMetaId("meta21");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION);
obj = d.getElementByMetaId("meta22");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_INITIAL_ASSIGNMENT);
obj = d.getElementByMetaId("meta23");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_INITIAL_ASSIGNMENT);
obj = d.getElementByMetaId("meta24");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_RULE);
obj = d.getElementByMetaId("meta25");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_RATE_RULE);
obj = d.getElementByMetaId("meta26");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE);
obj = d.getElementByMetaId("meta27");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_LOCAL_PARAMETER);
obj = d.getElementByMetaId("meta28");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LOCAL_PARAMETER);
obj = d.getElementByMetaId("meta29");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_UNIT_DEFINITION);
obj = d.getElementByMetaId("meta30");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_UNIT_DEFINITION);
obj = d.getElementByMetaId("meta31");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_UNIT);
obj = d.getElementByMetaId("meta32");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_UNIT);
obj = d.getElementByMetaId("meta33");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_PARAMETER);
obj = d.getElementByMetaId("meta34");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_LIST_OF);
assertTrue(((ListOf)obj).getItemTypeCode() == libsbml.SBML_MODIFIER_SPECIES_REFERENCE);
obj = d.getElementByMetaId("meta35");
assertTrue(obj != null);
assertTrue(obj.getTypeCode() == libsbml.SBML_MODIFIER_SPECIES_REFERENCE);
d = null;
}