public void test_ModifierSpeciesReference()
{
ModifierSpeciesReference msr = new ModifierSpeciesReference(2, 4);
assertEquals(true, msr.hasRequiredElements());
msr = null;
}
public void test_ModifierSpeciesReference()
{
ModifierSpeciesReference msr = new ModifierSpeciesReference(2, 4);
assertEquals(false, (msr.hasRequiredAttributes()));
msr.setSpecies("msr");
assertEquals(true, msr.hasRequiredAttributes());
msr = null;
}
public void test_SpeciesReference_Modifier_parent_create()
{
Reaction r = new Reaction(2, 4);
ModifierSpeciesReference sr = r.createModifier();
ListOf lo = r.getListOfModifiers();
assertTrue(lo == sr.getParentSBMLObject());
assertTrue(lo == r.getModifier(0).getParentSBMLObject());
assertTrue(r == lo.getParentSBMLObject());
}
/// <summary>
/// Checks if a given Modifier is present in the given compartment.
/// </summary>
private bool ModifierInDifferentCompartment(string reactionCompartment, ModifierSpeciesReference modifier, Model model)
{
var species = GetSpeciesById(modifier.getSpecies(), model);
if (species == null)
{
return(false);
}
return(species.getCompartment() != reactionCompartment);
}
public void test_Model_createModifier()
{
Model m = new Model(2, 2);
Reaction p = m.createReaction();
ModifierSpeciesReference sr = m.createModifier();
assertTrue(p.getNumModifiers() == 1);
assertTrue((sr).getLevel() == 2);
assertTrue((sr).getVersion() == 2);
m = null;
}
public void test_SpeciesReference_Modifier_parent_add()
{
ModifierSpeciesReference sr = new ModifierSpeciesReference(2, 4);
sr.setSpecies("s");
Reaction r = new Reaction(2, 4);
r.addModifier(sr);
sr = null;
ListOf lo = r.getListOfModifiers();
assertTrue(lo == r.getModifier(0).getParentSBMLObject());
assertTrue(r == lo.getParentSBMLObject());
}
public void test_SpeciesReference_Modifier_ancestor_create()
{
Reaction r = new Reaction(2, 4);
ModifierSpeciesReference sr = r.createModifier();
ListOf lo = r.getListOfModifiers();
assertTrue(sr.getAncestorOfType(libsbml.SBML_REACTION) == r);
assertTrue(sr.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(sr.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(sr.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
ModifierSpeciesReference obj = r.getModifier(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_REACTION) == r);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
}
public void test_SpeciesReference_Modifier_ancestor_add()
{
ModifierSpeciesReference sr = new ModifierSpeciesReference(2, 4);
sr.setSpecies("s");
Reaction r = new Reaction(2, 4);
r.addModifier(sr);
sr = null;
ListOf lo = r.getListOfModifiers();
ModifierSpeciesReference obj = r.getModifier(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_REACTION) == r);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
}
public void test_ModifierSpeciesReference_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2, 1);
sbmlns.addNamespaces(xmlns);
SBase object1 = new ModifierSpeciesReference(sbmlns);
assertTrue(object1.getTypeCode() == libsbml.SBML_MODIFIER_SPECIES_REFERENCE);
assertTrue(object1.getMetaId() == "");
assertTrue(object1.getNotes() == null);
assertTrue(object1.getAnnotation() == null);
assertTrue(object1.getLevel() == 2);
assertTrue(object1.getVersion() == 1);
assertTrue(object1.getNamespaces() != null);
XMLNamespaces n = object1.getNamespaces();
assertTrue(n.getLength() == 2);
object1 = 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 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 void ModifierSpeciesReferenceElement(Hashtable attrs)
{
String speciesId;
Species species;
try
{
speciesId = (String)attrs["species"];
species = (Species)this.model.findObject(speciesId);
ModifierSpeciesReference modifierRef;
List<ModifierSpeciesReference> modifierList;
Reaction reaction = (Reaction)elementStack.Peek();
modifierList = reaction.listOfModifiers;
modifierRef = new ModifierSpeciesReference(this.model, species);
modifierList.Add(modifierRef);
}
catch (Exception e)
{
Console.WriteLine("modifierSpeciesReference element missing required attribute 'species'");
throw (e);
}
}
