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; }