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); } }