private void ImportInitialAssignment(InitialAssignment initialAssignment, Model model)
{
var symbol = initialAssignment.getSymbol();
if (IsParameter(symbol))
{
var parameter = GetParameter(symbol);
SetPSV(initialAssignment.getMath(), parameter, String.Empty);
return;
}
if (IsContainerSizeParameter(symbol))
{
var sizeParameter = GetContainerSizeParameter(symbol);
SetPSV(initialAssignment.getMath(), sizeParameter, symbol);
return;
}
if (IsSpeciesAssignment(symbol))
{
DoSpeciesAssignment(symbol, initialAssignment.getMath(), isInitialAssignment: true);
}
CheckSpeciesReferences(initialAssignment.getId(), symbol, model);
}
public void test_Model_createInitialAssignment()
{
InitialAssignment c = M.createInitialAssignment();
assertTrue(c != null);
assertTrue(M.getNumInitialAssignments() == 1);
assertEquals(M.getInitialAssignment(0), c);
}
public void test_InitialAssignment()
{
InitialAssignment ia = new InitialAssignment(2, 4);
assertEquals(false, (ia.hasRequiredAttributes()));
ia.setSymbol("ia");
assertEquals(true, ia.hasRequiredAttributes());
ia = null;
}
public void test_InitialAssignment()
{
InitialAssignment ia = new InitialAssignment(2, 4);
assertEquals(false, (ia.hasRequiredElements()));
ia.setMath(libsbml.parseFormula("ia"));
assertEquals(true, ia.hasRequiredElements());
ia = null;
}
public void test_Model_addInitialAssignment3()
{
Model m = new Model(2, 2);
InitialAssignment ia = null;
int i = m.addInitialAssignment(ia);
assertTrue(i == libsbml.LIBSBML_OPERATION_FAILED);
assertTrue(m.getNumInitialAssignments() == 0);
m = null;
}
public void test_Model_createInitialAssignment()
{
Model m = new Model(2, 2);
InitialAssignment p = m.createInitialAssignment();
assertTrue(m.getNumInitialAssignments() == 1);
assertTrue((p).getLevel() == 2);
assertTrue((p).getVersion() == 2);
m = null;
}
public void test_InitialAssignment_parent_create()
{
Model m = new Model(2, 4);
InitialAssignment ia = m.createInitialAssignment();
ListOf lo = m.getListOfInitialAssignments();
assertTrue(lo == m.getInitialAssignment(0).getParentSBMLObject());
assertTrue(lo == ia.getParentSBMLObject());
assertTrue(m == lo.getParentSBMLObject());
}
public void setUp()
{
E = new InitialAssignment(2, 4);
if (E == null)
{
;
}
{
}
}
public void test_InitialAssignment_parent_NULL()
{
SBMLDocument d = new SBMLDocument();
Model m = d.createModel();
InitialAssignment c = m.createInitialAssignment();
InitialAssignment c1 = c.clone();
d = null;
assertTrue(c1.getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(c1.getParentSBMLObject() == null);
assertEquals(c1.getSBMLDocument(), null);
c1 = null;
}
public void test_InitialAssignment_copyConstructor()
{
InitialAssignment o1 = new InitialAssignment(2, 4);
o1.setSymbol("c");
assertTrue(o1.getId() == "c");
InitialAssignment o2 = new InitialAssignment(o1);
assertTrue(o2.getId() == "c");
assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject());
o2 = null;
o1 = null;
}
public void test_Model_addInitialAssignment2()
{
Model m = new Model(2, 2);
InitialAssignment ia = new InitialAssignment(2, 3);
ia.setSymbol("i");
ia.setMath(libsbml.parseFormula("gg"));
int i = m.addInitialAssignment(ia);
assertTrue(i == libsbml.LIBSBML_VERSION_MISMATCH);
assertTrue(m.getNumInitialAssignments() == 0);
ia = null;
m = null;
}
public void test_InitialAssignment_parent_add()
{
InitialAssignment ia = new InitialAssignment(2, 4);
Model m = new Model(2, 4);
ia.setSymbol("c");
ia.setMath(libsbml.parseFormula("9"));
m.addInitialAssignment(ia);
ia = null;
ListOf lo = m.getListOfInitialAssignments();
assertTrue(lo == m.getInitialAssignment(0).getParentSBMLObject());
assertTrue(m == lo.getParentSBMLObject());
}
public void test_InitialAssignment_ancestor_create()
{
Model m = new Model(2, 4);
InitialAssignment ia = m.createInitialAssignment();
ListOf lo = m.getListOfInitialAssignments();
assertTrue(ia.getAncestorOfType(libsbml.SBML_MODEL) == m);
assertTrue(ia.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(ia.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(ia.getAncestorOfType(libsbml.SBML_EVENT) == null);
InitialAssignment obj = m.getInitialAssignment(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_MODEL) == m);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_EVENT) == null);
}
public void test_Model_addInitialAssignment1()
{
Model m = new Model(2, 2);
InitialAssignment ia = new InitialAssignment(2, 2);
int i = m.addInitialAssignment(ia);
assertTrue(i == libsbml.LIBSBML_INVALID_OBJECT);
ia.setSymbol("i");
i = m.addInitialAssignment(ia);
assertTrue(i == libsbml.LIBSBML_INVALID_OBJECT);
ia.setMath(libsbml.parseFormula("gg"));
i = m.addInitialAssignment(ia);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(m.getNumInitialAssignments() == 1);
ia = null;
m = null;
}
public void test_InitialAssignment_ancestor_add()
{
InitialAssignment ia = new InitialAssignment(2, 4);
Model m = new Model(2, 4);
ia.setSymbol("c");
ia.setMath(libsbml.parseFormula("9"));
m.addInitialAssignment(ia);
ia = null;
ListOf lo = m.getListOfInitialAssignments();
InitialAssignment obj = m.getInitialAssignment(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_MODEL) == m);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_EVENT) == null);
}
protected override string GetHeader()
{
if (InitialAssignment == null)
{
throw new MissingMandatoryElementException("Initial declaration is required in loop statement");
}
if (BreakCondition == null)
{
throw new MissingMandatoryElementException("Break condition is required in loop statement");
}
if (StepInstruction == null)
{
throw new MissingMandatoryElementException("Step instruction is required in loop statement");
}
return($"for ({InitialAssignment.GenerateCode()}; {BreakCondition.GenerateCode()}; {StepInstruction.GenerateCode()}) {{\n");
}
public void test_InitialAssignment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2, 3);
sbmlns.addNamespaces(xmlns);
InitialAssignment object1 = new InitialAssignment(sbmlns);
assertTrue(object1.getTypeCode() == libsbml.SBML_INITIAL_ASSIGNMENT);
assertTrue(object1.getMetaId() == "");
assertTrue(object1.getNotes() == null);
assertTrue(object1.getAnnotation() == null);
assertTrue(object1.getLevel() == 2);
assertTrue(object1.getVersion() == 3);
assertTrue(object1.getNamespaces() != null);
assertTrue(object1.getNamespaces().getLength() == 2);
object1 = null;
}
public void test_Model_addInitialAssignment4()
{
Model m = new Model(2, 2);
InitialAssignment ia = new InitialAssignment(2, 2);
ia.setSymbol("ia");
ia.setMath(libsbml.parseFormula("a+b"));
InitialAssignment ia1 = new InitialAssignment(2, 2);
ia1.setSymbol("ia");
ia1.setMath(libsbml.parseFormula("a+b"));
int i = m.addInitialAssignment(ia);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(m.getNumInitialAssignments() == 1);
i = m.addInitialAssignment(ia1);
assertTrue(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID);
assertTrue(m.getNumInitialAssignments() == 1);
ia = null;
ia1 = null;
m = null;
}
public void tearDown()
{
E = null;
}
static void testListOfRemove(ListOf lof, SBase s)
{
string ename = s.getElementName();
lof.append(s);
SBase c = lof.get(0);
if (c is CompartmentType)
{
CompartmentType x = (lof as ListOfCompartmentTypes).remove(0); c = x;
}
else if (c is Compartment)
{
Compartment x = (lof as ListOfCompartments).remove(0); c = x;
}
else if (c is Constraint)
{
Constraint x = (lof as ListOfConstraints).remove(0); c = x;
}
else if (c is EventAssignment)
{
EventAssignment x = (lof as ListOfEventAssignments).remove(0); c = x;
}
else if (c is Event)
{
Event x = (lof as ListOfEvents).remove(0); c = x;
}
else if (c is FunctionDefinition)
{
FunctionDefinition x = (lof as ListOfFunctionDefinitions).remove(0); c = x;
}
else if (c is InitialAssignment)
{
InitialAssignment x = (lof as ListOfInitialAssignments).remove(0); c = x;
}
else if (c is Parameter)
{
Parameter x = (lof as ListOfParameters).remove(0); c = x;
}
else if (c is Reaction)
{
Reaction x = (lof as ListOfReactions).remove(0); c = x;
}
else if (c is Rule)
{
Rule x = (lof as ListOfRules).remove(0); c = x;
}
else if (c is Species)
{
Species x = (lof as ListOfSpecies).remove(0); c = x;
}
else if (c is SpeciesReference)
{
SimpleSpeciesReference x = (lof as ListOfSpeciesReferences).remove(0); c = x;
}
else if (c is SpeciesType)
{
SpeciesType x = (lof as ListOfSpeciesTypes).remove(0); c = x;
}
else if (c is UnitDefinition)
{
UnitDefinition x = (lof as ListOfUnitDefinitions).remove(0); c = x;
}
else if (c is Unit)
{
Unit x = (lof as ListOfUnits).remove(0); c = x;
}
else
{
ERR("[testListOfRemove] Error: (" + ename + ") : ListOfXXX::remove() failed.");
return;
}
if (c == null)
{
ERR("[testListOfRemove] Error: (" + ename + ") : ListOfXXX::remove() failed.");
return;
}
string enameGet = c.getElementName();
if (ename == enameGet)
{
//Console.Out.WriteLine("[testListOfRemove] OK: (" + ename + ") remove(" + enameGet + ") : type match.");
OK();
}
else
{
ERR("[testListOfRemove] Error: (" + ename + ") remove(" + enameGet + ") : type mismatch.");
}
}
static void testClone(SBase s)
{
string ename = s.getElementName();
SBase c = s.clone();
if (c is Compartment)
{
Compartment x = (s as Compartment).clone(); c = x;
}
else if (c is CompartmentType)
{
CompartmentType x = (s as CompartmentType).clone(); c = x;
}
else if (c is Constraint)
{
Constraint x = (s as Constraint).clone(); c = x;
}
else if (c is Delay)
{
Delay x = (s as Delay).clone(); c = x;
}
else if (c is Event)
{
Event x = (s as Event).clone(); c = x;
}
else if (c is EventAssignment)
{
EventAssignment x = (s as EventAssignment).clone(); c = x;
}
else if (c is FunctionDefinition)
{
FunctionDefinition x = (s as FunctionDefinition).clone(); c = x;
}
else if (c is InitialAssignment)
{
InitialAssignment x = (s as InitialAssignment).clone(); c = x;
}
else if (c is KineticLaw)
{
KineticLaw x = (s as KineticLaw).clone(); c = x;
}
// currently return type of ListOf::clone() is SBase
else if (c is ListOf)
{
SBase x = (s as ListOf).clone(); c = x;
}
else if (c is Model)
{
Model x = (s as Model).clone(); c = x;
}
else if (c is Parameter)
{
Parameter x = (s as Parameter).clone(); c = x;
}
else if (c is Reaction)
{
Reaction x = (s as Reaction).clone(); c = x;
}
else if (c is AlgebraicRule)
{
AlgebraicRule x = (s as AlgebraicRule).clone(); c = x;
}
else if (c is AssignmentRule)
{
AssignmentRule x = (s as AssignmentRule).clone(); c = x;
}
else if (c is RateRule)
{
RateRule x = (s as RateRule).clone(); c = x;
}
else if (c is SBMLDocument)
{
SBMLDocument x = (s as SBMLDocument).clone(); c = x;
}
else if (c is Species)
{
Species x = (s as Species).clone(); c = x;
}
else if (c is SpeciesReference)
{
SpeciesReference x = (s as SpeciesReference).clone(); c = x;
}
else if (c is SpeciesType)
{
SpeciesType x = (s as SpeciesType).clone(); c = x;
}
else if (c is SpeciesReference)
{
SpeciesReference x = (s as SpeciesReference).clone(); c = x;
}
else if (c is StoichiometryMath)
{
StoichiometryMath x = (s as StoichiometryMath).clone(); c = x;
}
else if (c is Trigger)
{
Trigger x = (s as Trigger).clone(); c = x;
}
else if (c is Unit)
{
Unit x = (s as Unit).clone(); c = x;
}
else if (c is UnitDefinition)
{
UnitDefinition x = (s as UnitDefinition).clone(); c = x;
}
else if (c is ListOfCompartmentTypes)
{
ListOfCompartmentTypes x = (s as ListOfCompartmentTypes).clone(); c = x;
}
else if (c is ListOfCompartments)
{
ListOfCompartments x = (s as ListOfCompartments).clone(); c = x;
}
else if (c is ListOfConstraints)
{
ListOfConstraints x = (s as ListOfConstraints).clone(); c = x;
}
else if (c is ListOfEventAssignments)
{
ListOfEventAssignments x = (s as ListOfEventAssignments).clone(); c = x;
}
else if (c is ListOfEvents)
{
ListOfEvents x = (s as ListOfEvents).clone(); c = x;
}
else if (c is ListOfFunctionDefinitions)
{
ListOfFunctionDefinitions x = (s as ListOfFunctionDefinitions).clone(); c = x;
}
else if (c is ListOfInitialAssignments)
{
ListOfInitialAssignments x = (s as ListOfInitialAssignments).clone(); c = x;
}
else if (c is ListOfParameters)
{
ListOfParameters x = (s as ListOfParameters).clone(); c = x;
}
else if (c is ListOfReactions)
{
ListOfReactions x = (s as ListOfReactions).clone(); c = x;
}
else if (c is ListOfRules)
{
ListOfRules x = (s as ListOfRules).clone(); c = x;
}
else if (c is ListOfSpecies)
{
ListOfSpecies x = (s as ListOfSpecies).clone(); c = x;
}
else if (c is ListOfSpeciesReferences)
{
ListOfSpeciesReferences x = (s as ListOfSpeciesReferences).clone(); c = x;
}
else if (c is ListOfSpeciesTypes)
{
ListOfSpeciesTypes x = (s as ListOfSpeciesTypes).clone(); c = x;
}
else if (c is ListOfUnitDefinitions)
{
ListOfUnitDefinitions x = (s as ListOfUnitDefinitions).clone(); c = x;
}
else if (c is ListOfUnits)
{
ListOfUnits x = (s as ListOfUnits).clone(); c = x;
}
else
{
ERR("[testClone] Error: (" + ename + ") : clone() failed.");
return;
}
if (c == null)
{
ERR("[testClone] Error: (" + ename + ") : clone() failed.");
return;
}
string enameClone = c.getElementName();
if (ename == enameClone)
{
//Console.Out.WriteLine("[testClone] OK: (" + ename + ") clone(" + enameClone + ") : type match.");
OK();
}
else
{
ERR("[testClone] Error: (" + ename + ") clone(" + enameClone + ") : type mismatch.");
}
}
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("Usage: printUnits filename");
return(1);
}
string filename = args[0];
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors() > 0)
{
Console.Error.WriteLine("Encountered the following SBML errors:");
document.printErrors();
return(1);
}
Model model = document.getModel();
if (model == null)
{
Console.WriteLine("No model present.");
return(1);
}
int i, j;
for (i = 0; i < model.getNumSpecies(); i++)
{
Species s = model.getSpecies(i);
Console.WriteLine("Species " + i + ": "
+ UnitDefinition.printUnits(s.getDerivedUnitDefinition()));
}
for (i = 0; i < model.getNumCompartments(); i++)
{
Compartment c = model.getCompartment(i);
Console.WriteLine("Compartment " + i + ": "
+ UnitDefinition.printUnits(c.getDerivedUnitDefinition()))
;
}
for (i = 0; i < model.getNumParameters(); i++)
{
Parameter p = model.getParameter(i);
Console.WriteLine("Parameter " + i + ": "
+ UnitDefinition.printUnits(p.getDerivedUnitDefinition()))
;
}
for (i = 0; i < model.getNumInitialAssignments(); i++)
{
InitialAssignment ia = model.getInitialAssignment(i);
Console.WriteLine("InitialAssignment " + i + ": "
+ UnitDefinition.printUnits(ia.getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((ia.containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
for (i = 0; i < model.getNumEvents(); i++)
{
Event e = model.getEvent(i);
Console.WriteLine("Event " + i + ": ");
if (e.isSetDelay())
{
Console.WriteLine("Delay: "
+ UnitDefinition.printUnits(e.getDelay().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((e.getDelay().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
for (j = 0; j < e.getNumEventAssignments(); j++)
{
EventAssignment ea = e.getEventAssignment(j);
Console.WriteLine("EventAssignment " + j + ": "
+ UnitDefinition.printUnits(ea.getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((ea.containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
}
for (i = 0; i < model.getNumReactions(); i++)
{
Reaction r = model.getReaction(i);
Console.WriteLine("Reaction " + i + ": ");
if (r.isSetKineticLaw())
{
Console.WriteLine("Kinetic Law: "
+ UnitDefinition.printUnits(r.getKineticLaw().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((r.getKineticLaw().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
for (j = 0; j < r.getNumReactants(); j++)
{
SpeciesReference sr = r.getReactant(j);
if (sr.isSetStoichiometryMath())
{
Console.WriteLine("Reactant stoichiometryMath" + j + ": "
+ UnitDefinition.printUnits(sr.getStoichiometryMath().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((sr.getStoichiometryMath().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
}
for (j = 0; j < r.getNumProducts(); j++)
{
SpeciesReference sr = r.getProduct(j);
if (sr.isSetStoichiometryMath())
{
Console.WriteLine("Product stoichiometryMath" + j + ": "
+ UnitDefinition.printUnits(sr.getStoichiometryMath().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((sr.getStoichiometryMath().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
}
}
for (i = 0; i < model.getNumRules(); i++)
{
Rule r = model.getRule(i);
Console.WriteLine("Rule " + i + ": "
+ UnitDefinition.printUnits(r.getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((r.containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
return(0);
}
public void tearDown()
{
IA = null;
}
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("Usage: printNotes filename");
return(1);
}
int i, j;
string filename = args[0];
SBMLDocument document;
document = libsbml.readSBML(filename);
int errors = (int)document.getNumErrors();
Console.WriteLine();
Console.WriteLine("filename: " + filename);
Console.WriteLine();
if (errors > 0)
{
document.printErrors();
return(errors);
}
/* Model */
Model m = document.getModel();
printNotes(m);
for (i = 0; i < m.getNumReactions(); i++)
{
Reaction re = m.getReaction(i);
printNotes(re);
/* SpeciesReference (Reacatant) */
for (j = 0; j < re.getNumReactants(); j++)
{
SpeciesReference rt = re.getReactant(j);
if (rt.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(rt, (rt.isSetSpecies() ? rt.getSpecies() : ""));
}
/* SpeciesReference (Product) */
for (j = 0; j < re.getNumProducts(); j++)
{
SpeciesReference rt = re.getProduct(j);
if (rt.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(rt, (rt.isSetSpecies() ? rt.getSpecies() : ""));
}
/* ModifierSpeciesReference (Modifier) */
for (j = 0; j < re.getNumModifiers(); j++)
{
ModifierSpeciesReference md = re.getModifier(j);
if (md.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(md, (md.isSetSpecies() ? md.getSpecies() : ""));
}
/* Kineticlaw */
if (re.isSetKineticLaw())
{
KineticLaw kl = re.getKineticLaw();
if (kl.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(kl);
/* Parameter */
for (j = 0; j < kl.getNumParameters(); j++)
{
Parameter pa = kl.getParameter(j);
if (pa.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(pa);
}
}
}
/* Species */
for (i = 0; i < m.getNumSpecies(); i++)
{
Species sp = m.getSpecies(i);
printNotes(sp);
}
/* Compartment */
for (i = 0; i < m.getNumCompartments(); i++)
{
Compartment sp = m.getCompartment(i);
printNotes(sp);
}
/* FunctionDefinition */
for (i = 0; i < m.getNumFunctionDefinitions(); i++)
{
FunctionDefinition sp = m.getFunctionDefinition(i);
printNotes(sp);
}
/* UnitDefinition */
for (i = 0; i < m.getNumUnitDefinitions(); i++)
{
UnitDefinition sp = m.getUnitDefinition(i);
printNotes(sp);
}
/* Parameter */
for (i = 0; i < m.getNumParameters(); i++)
{
Parameter sp = m.getParameter(i);
printNotes(sp);
}
/* Rule */
for (i = 0; i < m.getNumRules(); i++)
{
Rule sp = m.getRule(i);
printNotes(sp);
}
/* InitialAssignment */
for (i = 0; i < m.getNumInitialAssignments(); i++)
{
InitialAssignment sp = m.getInitialAssignment(i);
printNotes(sp);
}
/* Event */
for (i = 0; i < m.getNumEvents(); i++)
{
Event sp = m.getEvent(i);
printNotes(sp);
/* Trigger */
if (sp.isSetTrigger())
{
Trigger tg = sp.getTrigger();
if (tg.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(tg);
}
/* Delay */
if (sp.isSetDelay())
{
Delay dl = sp.getDelay();
if (dl.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(dl);
}
/* EventAssignment */
for (j = 0; j < sp.getNumEventAssignments(); j++)
{
EventAssignment ea = sp.getEventAssignment(j);
if (ea.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(ea);
}
}
/* SpeciesType */
for (i = 0; i < m.getNumSpeciesTypes(); i++)
{
SpeciesType sp = m.getSpeciesType(i);
printNotes(sp);
}
/* Constraint */
for (i = 0; i < m.getNumConstraints(); i++)
{
Constraint sp = m.getConstraint(i);
printNotes(sp);
}
return(errors);
}
public void InitialAssignmentElement(Hashtable attrs)
{
String symbol;
SBase variable = null;
if (attrs.Contains("symbol"))
{
symbol = (String)attrs["symbol"];
if (this.model.findObject(symbol)!=null)
variable = (SBase)this.model.findObject(symbol);
InitialAssignment initialAssignment = new InitialAssignment(this.model, variable);
this.model.listOfInitialAssignments.Add(initialAssignment);
elementStack.Push(initialAssignment);
}
// else throw exception on required attribute
}
public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.Write(Environment.NewLine + "Usage: unsetAnnotation <input-filename> <output-filename>" + Environment.NewLine + Environment.NewLine);
return 1;
}
int i, j;
string filename = args[0];
SBMLDocument document;
document = libsbml.readSBML(filename);
int errors = (int)document.getNumErrors();
if (errors > 0)
{
document.printErrors();
return errors;
}
Model m = document.getModel();
m.unsetAnnotation();
for (i = 0; i < m.getNumReactions(); i++)
{
Reaction re = m.getReaction(i);
re.unsetAnnotation();
for (j = 0; j < re.getNumReactants(); j++)
{
SpeciesReference rt = re.getReactant(j);
rt.unsetAnnotation();
}
for (j = 0; j < re.getNumProducts(); j++)
{
SpeciesReference rt = re.getProduct(j);
rt.unsetAnnotation();
}
for (j = 0; j < re.getNumModifiers(); j++)
{
ModifierSpeciesReference md = re.getModifier(j);
md.unsetAnnotation();
}
if (re.isSetKineticLaw())
{
KineticLaw kl = re.getKineticLaw();
kl.unsetAnnotation();
for (j = 0; j < kl.getNumParameters(); j++)
{
Parameter pa = kl.getParameter(j);
pa.unsetAnnotation();
}
}
}
for (i = 0; i < m.getNumSpecies(); i++)
{
Species sp = m.getSpecies(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumCompartments(); i++)
{
Compartment sp = m.getCompartment(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumFunctionDefinitions(); i++)
{
FunctionDefinition sp = m.getFunctionDefinition(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumUnitDefinitions(); i++)
{
UnitDefinition sp = m.getUnitDefinition(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumParameters(); i++)
{
Parameter sp = m.getParameter(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumRules(); i++)
{
Rule sp = m.getRule(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumInitialAssignments(); i++)
{
InitialAssignment sp = m.getInitialAssignment(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumEvents(); i++)
{
Event sp = m.getEvent(i);
sp.unsetAnnotation();
for (j = 0; j < sp.getNumEventAssignments(); j++)
{
EventAssignment ea = sp.getEventAssignment(j);
ea.unsetAnnotation();
}
}
for (i = 0; i < m.getNumSpeciesTypes(); i++)
{
SpeciesType sp = m.getSpeciesType(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumConstraints(); i++)
{
Constraint sp = m.getConstraint(i);
sp.unsetAnnotation();
}
libsbml.writeSBML(document, args[1]);
return errors;
}
public static void Main(string[] args)
{
ArraysPkgNamespaces arraysNs = new ArraysPkgNamespaces();
SBMLDocument doc = new SBMLDocument(arraysNs);
doc.setPackageRequired("arrays", true);
Model model = doc.createModel();
// create parameters
Parameter param = model.createParameter();
param.setId("n");
param.setValue(10);
param.setConstant(true);
param = model.createParameter();
param.setId("m");
param.setValue(10);
param.setConstant(true);
param = model.createParameter();
param.setId("x");
param.setValue(5.7);
param.setConstant(true);
ArraysSBasePlugin paramPlugin = (ArraysSBasePlugin)param.getPlugin("arrays");
Dimension dim = paramPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
param = model.createParameter();
param.setId("y");
param.setConstant(false);
paramPlugin = (ArraysSBasePlugin)param.getPlugin("arrays");
dim = paramPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
param = model.createParameter();
param.setId("z");
param.setConstant(false);
paramPlugin = (ArraysSBasePlugin)param.getPlugin("arrays");
dim = paramPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create initial assignments
InitialAssignment assignment = model.createInitialAssignment();
assignment.setSymbol("y");
ASTNode ast = new ASTNode(libsbml.AST_REAL);
ast.setValue(3.2);
assignment.setMath(ast);
assignment = model.createInitialAssignment();
assignment.setSymbol("z");
ast = new ASTNode(libsbml.AST_REAL);
ast.setValue(5.7);
assignment.setMath(ast);
ArraysSBasePlugin assignmentPlugin = (ArraysSBasePlugin)assignment.getPlugin("arrays");
dim = assignmentPlugin.createDimension();
dim.setId("i");
dim.setSize("m");
Index index = assignmentPlugin.createIndex();
ASTNode newAst = new ASTNode(libsbml.AST_FUNCTION);
newAst.setName("selector");
ASTNode ci = new ASTNode(libsbml.AST_NAME);
ci.setName("z");
newAst.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
newAst.addChild(ci);
index.setMath(newAst);
assignment = model.createInitialAssignment();
assignment.setSymbol("z");
ast = new ASTNode(libsbml.AST_REAL);
ast.setValue(3.2);
assignment.setMath(ast);
assignmentPlugin = (ArraysSBasePlugin)assignment.getPlugin("arrays");
dim = assignmentPlugin.createDimension();
dim.setId("i");
dim.setSize("m");
index = assignmentPlugin.createIndex();
newAst = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("z");
newAst.addChild(ci);
ASTNode plus = new ASTNode(libsbml.AST_PLUS);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
plus.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("m");
plus.addChild(ci);
newAst.addChild(plus);
index.setMath(newAst);
libsbml.writeSBMLToFile(doc, "arrays2.xml");
}
