public void test_KineticLaw_getParameterById()
{
Parameter k1 = new Parameter(2, 4);
Parameter k2 = new Parameter(2, 4);
k1.setId("k1");
k2.setId("k2");
k1.setValue(3.14);
k2.setValue(2.72);
M.addParameter(k1);
M.addParameter(k2);
Reaction r1 = new Reaction(2, 4);
r1.setId("reaction_1");
KineticLaw kl = new KineticLaw(2, 4);
kl.setFormula("k1 * X0");
Parameter k3 = new Parameter(2, 4);
Parameter k4 = new Parameter(2, 4);
k3.setId("k1");
k4.setId("k2");
k3.setValue(2.72);
k4.setValue(3.14);
kl.addParameter(k3);
kl.addParameter(k4);
r1.setKineticLaw(kl);
M.addReaction(r1);
KineticLaw kl1 = M.getReaction(0).getKineticLaw();
assertNotEquals(kl1.getParameter("k1"), k3);
assertNotEquals(kl1.getParameter("k1"), k1);
assertNotEquals(kl1.getParameter("k2"), k4);
assertEquals(kl1.getParameter("k3"), null);
}
public void test_KineticLaw_parent_NULL()
{
Reaction r = new Reaction(2, 4);
KineticLaw kl = r.createKineticLaw();
Parameter p = kl.createParameter();
assertTrue(r == kl.getParentSBMLObject());
assertTrue(r == p.getAncestorOfType(libsbml.SBML_REACTION));
assertTrue(kl == p.getAncestorOfType(libsbml.SBML_KINETIC_LAW));
KineticLaw kl1 = kl.clone();
assertTrue(kl1.getParentSBMLObject() == null);
assertTrue(kl1.getParameter(0).getAncestorOfType(libsbml.SBML_REACTION) == null);
assertTrue(kl1 == kl1.getParameter(0).getAncestorOfType(libsbml.SBML_KINETIC_LAW));
r = null;
}
public void test_KineticLaw_Parameter_parent_add()
{
KineticLaw kl = new KineticLaw(2, 4);
Parameter p = new Parameter(2, 4);
p.setId("jake");
kl.addParameter(p);
p = null;
assertTrue(kl.getNumParameters() == 1);
assertTrue(kl.getParameter(0).getId() == "jake");
ListOfParameters lop = kl.getListOfParameters();
assertTrue(kl == lop.getParentSBMLObject());
assertTrue(lop == kl.getParameter(0).getParentSBMLObject());
kl = null;
}
public void test_KineticLaw_Parameter_ancestor_create_model()
{
Model m = new Model(2, 4);
Reaction r = m.createReaction();
KineticLaw kl = m.createKineticLaw();
Parameter p = m.createKineticLawParameter();
assertTrue(kl.getNumParameters() == 1);
ListOfParameters lop = kl.getListOfParameters();
assertTrue(p.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl);
assertTrue(p.getAncestorOfType(libsbml.SBML_LIST_OF) == lop);
assertTrue(p.getAncestorOfType(libsbml.SBML_REACTION) == r);
assertTrue(p.getAncestorOfType(libsbml.SBML_MODEL) == m);
assertTrue(p.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(p.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
Parameter obj = kl.getParameter(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lop);
assertTrue(obj.getAncestorOfType(libsbml.SBML_REACTION) == r);
assertTrue(obj.getAncestorOfType(libsbml.SBML_MODEL) == m);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
kl = null;
}
public void test_KineticLaw_getParameter()
{
Parameter k1 = new Parameter(2, 4);
Parameter k2 = new Parameter(2, 4);
k1.setId("k1");
k2.setId("k2");
k1.setValue(3.14);
k2.setValue(2.72);
kl.addParameter(k1);
kl.addParameter(k2);
k1 = null;
k2 = null;
assertTrue(kl.getNumParameters() == 2);
k1 = kl.getParameter(0);
k2 = kl.getParameter(1);
assertTrue(("k1" == k1.getId()));
assertTrue(("k2" == k2.getId()));
assertTrue(k1.getValue() == 3.14);
assertTrue(k2.getValue() == 2.72);
}
public void test_KineticLaw_Parameter_parent_create()
{
KineticLaw kl = new KineticLaw(2, 4);
Parameter p = kl.createParameter();
assertTrue(kl.getNumParameters() == 1);
ListOfParameters lop = kl.getListOfParameters();
assertTrue(kl == lop.getParentSBMLObject());
assertTrue(lop == p.getParentSBMLObject());
assertTrue(lop == kl.getParameter(0).getParentSBMLObject());
kl = null;
}
public void test_KineticLaw_Parameter_parent_create_model()
{
Model m = new Model(2, 4);
Reaction r = m.createReaction();
KineticLaw kl = m.createKineticLaw();
Parameter p = m.createKineticLawParameter();
assertTrue(kl.getNumParameters() == 1);
ListOfParameters lop = kl.getListOfParameters();
assertTrue(r == kl.getParentSBMLObject());
assertTrue(kl == lop.getParentSBMLObject());
assertTrue(lop == p.getParentSBMLObject());
assertTrue(lop == kl.getParameter(0).getParentSBMLObject());
kl = null;
}
public void test_KineticLaw_Parameter_ancestor_add()
{
KineticLaw kl = new KineticLaw(2, 4);
Parameter p = new Parameter(2, 4);
p.setId("jake");
kl.addParameter(p);
p = null;
ListOfParameters lop = kl.getListOfParameters();
Parameter obj = kl.getParameter(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lop);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
kl = null;
}
public void test_KineticLaw_copyConstructor()
{
KineticLaw o1 = new KineticLaw(2, 4);
Parameter p = new Parameter(2, 4);
p.setId("jake");
o1.addParameter(p);
p = null;
assertTrue(o1.getNumParameters() == 1);
assertTrue(o1.getParameter(0).getId() == "jake");
KineticLaw o2 = new KineticLaw(o1);
assertTrue(o2.getNumParameters() == 1);
assertTrue(o2.getParameter(0).getId() == "jake");
assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject());
o2 = null;
o1 = null;
}
public void test_KineticLaw_Parameter_ancestor_create()
{
KineticLaw kl = new KineticLaw(2, 4);
Parameter p = kl.createParameter();
assertTrue(kl.getNumParameters() == 1);
ListOfParameters lop = kl.getListOfParameters();
assertTrue(p.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl);
assertTrue(p.getAncestorOfType(libsbml.SBML_LIST_OF) == lop);
assertTrue(p.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(p.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
Parameter obj = kl.getParameter(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lop);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
kl = 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;
}
