END_TEST START_TEST (test_L3_KineticLaw_addParameter2) { KineticLaw_t *kl = KineticLaw_create(3, 1); LocalParameter_t *lp = LocalParameter_create(3, 1); LocalParameter_t *lp1 = LocalParameter_create(3, 1); int i = KineticLaw_addLocalParameter(kl, lp); fail_unless( i == LIBSBML_INVALID_OBJECT); LocalParameter_setId(lp, "p"); LocalParameter_setId(lp1, "p1"); i = KineticLaw_addLocalParameter(kl, lp); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( KineticLaw_getNumParameters(kl) == 1); fail_unless( KineticLaw_getNumLocalParameters(kl) == 1); i = KineticLaw_addParameter(kl, (Parameter_t *)lp1); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( KineticLaw_getNumParameters(kl) == 2); fail_unless( KineticLaw_getNumLocalParameters(kl) == 2); LocalParameter_free(lp); LocalParameter_free(lp1); KineticLaw_free(kl); }
END_TEST START_TEST (test_L3_KineticLaw_addParameter1) { KineticLaw_t *kl = KineticLaw_create(3, 1); Parameter_t *p = Parameter_create(3, 1); int i = KineticLaw_addParameter(KL, p); fail_unless( i == LIBSBML_INVALID_OBJECT); Parameter_setId(p, "p"); i = KineticLaw_addParameter(KL, p); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( KineticLaw_getNumParameters(KL) == 1); fail_unless( KineticLaw_getNumLocalParameters(KL) == 1); fail_unless( KineticLaw_getNumParameters(kl) == 0); fail_unless( KineticLaw_getNumLocalParameters(kl) == 0); i = KineticLaw_addParameter(kl, p); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( KineticLaw_getNumParameters(KL) == 1); fail_unless( KineticLaw_getNumLocalParameters(KL) == 1); fail_unless( KineticLaw_getNumParameters(kl) == 1); fail_unless( KineticLaw_getNumLocalParameters(kl) == 1); Parameter_free(p); KineticLaw_free(kl); }
END_TEST START_TEST (test_KineticLaw_getParameterById) { Parameter_t *k1 = Parameter_create(2, 4); Parameter_t *k2 = Parameter_create(2, 4); Parameter_setId(k1, "k1"); Parameter_setId(k2, "k2"); Parameter_setValue(k1, 3.14); Parameter_setValue(k2, 2.72); KineticLaw_addParameter(kl, k1); KineticLaw_addParameter(kl, k2); Parameter_free(k1); Parameter_free(k2); fail_unless( KineticLaw_getNumParameters(kl) == 2 ); k1 = KineticLaw_getParameterById(kl, "k1"); k2 = KineticLaw_getParameterById(kl, "k2"); fail_unless( !strcmp(Parameter_getId(k1), "k1") ); fail_unless( !strcmp(Parameter_getId(k2), "k2") ); fail_unless( Parameter_getValue(k1) == 3.14 ); fail_unless( Parameter_getValue(k2) == 2.72 ); }
END_TEST START_TEST (test_KineticLaw_addParameter) { Parameter_t * p = Parameter_create(2, 4); Parameter_setId(p, "p"); KineticLaw_addParameter(kl, p); fail_unless( KineticLaw_getNumParameters(kl) == 1 ); Parameter_free(p); }
END_TEST START_TEST (test_KineticLaw_removeParameter) { Parameter_t *o1, *o2, *o3; o1 = KineticLaw_createParameter(kl); o2 = KineticLaw_createParameter(kl); o3 = KineticLaw_createParameter(kl); Parameter_setId(o3,"test"); fail_unless( KineticLaw_removeParameter(kl,0) == o1 ); fail_unless( KineticLaw_getNumParameters(kl) == 2 ); fail_unless( KineticLaw_removeParameter(kl,0) == o2 ); fail_unless( KineticLaw_getNumParameters(kl) == 1 ); fail_unless( KineticLaw_removeParameterById(kl,"test") == o3 ); fail_unless( KineticLaw_getNumParameters(kl) == 0 ); Parameter_free(o1); Parameter_free(o2); Parameter_free(o3); }
END_TEST START_TEST (test_KineticLaw_createParameter) { KineticLaw_t *kl = KineticLaw_create(2, 2); Parameter_t *p = KineticLaw_createParameter(kl); fail_unless( KineticLaw_getNumParameters(kl) == 1); fail_unless( SBase_getLevel((SBase_t *) (p)) == 2 ); fail_unless( SBase_getVersion((SBase_t *) (p)) == 2 ); KineticLaw_free(kl); }
END_TEST START_TEST (test_KineticLaw_addParameter4) { KineticLaw_t *kl = KineticLaw_create(2, 2); Parameter_t *p = NULL; int i = KineticLaw_addParameter(kl, p); fail_unless( i == LIBSBML_OPERATION_FAILED); fail_unless( KineticLaw_getNumParameters(kl) == 0); KineticLaw_free(kl); }
END_TEST START_TEST (test_KineticLaw_addParameter3) { KineticLaw_t *kl = KineticLaw_create(2, 2); Parameter_t *p = Parameter_create(1, 2); Parameter_setId(p, "p"); int i = KineticLaw_addParameter(kl, p); fail_unless( i == LIBSBML_LEVEL_MISMATCH); fail_unless( KineticLaw_getNumParameters(kl) == 0); Parameter_free(p); KineticLaw_free(kl); }
int main (int argc, char* argv[]) { unsigned int i,j,errors; const char* filename = argv[1]; SBMLDocument_t* document; Model_t* m; if (argc != 3) { printf("\nUsage: unsetNotes <input-filename> <output-filename>\n"); return 1; } filename = argv[1]; document = readSBML(filename); errors = SBMLDocument_getNumErrors(document); if(errors > 0) { SBMLDocument_printErrors(document, stderr); SBMLDocument_free(document); return errors; } m = SBMLDocument_getModel( document ); SBase_unsetNotes((SBase_t*)m); for(i=0; i < Model_getNumReactions(m); i++) { Reaction_t* re = Model_getReaction(m, i); SBase_unsetNotes((SBase_t*)re); for(j=0; j < Reaction_getNumReactants(re); j++) { SpeciesReference_t* rt = Reaction_getReactant(re,j); SBase_unsetNotes((SBase_t*)rt); } for(j=0; j < Reaction_getNumProducts(re); j++) { SpeciesReference_t* rt = Reaction_getProduct(re,j); SBase_unsetNotes((SBase_t*)rt); } for(j=0; j < Reaction_getNumModifiers(re); j++) { SpeciesReference_t* md = Reaction_getModifier(re,j); SBase_unsetNotes((SBase_t*)md); } if(Reaction_isSetKineticLaw(re)) { KineticLaw_t* kl = Reaction_getKineticLaw(re); SBase_unsetNotes((SBase_t*)kl); for(j=0; j < KineticLaw_getNumParameters(kl); j++) { Parameter_t* pa = KineticLaw_getParameter(kl, j); SBase_unsetNotes((SBase_t*)pa); } } } for(i=0; i < Model_getNumSpecies(m); i++) { Species_t* sp = Model_getSpecies(m, i); SBase_unsetNotes((SBase_t*)sp); } for(i=0; i < Model_getNumCompartments(m); i++) { Compartment_t* sp = Model_getCompartment(m,i); SBase_unsetNotes((SBase_t*)sp); } for(i=0; i < Model_getNumFunctionDefinitions(m); i++) { FunctionDefinition_t* sp = Model_getFunctionDefinition(m,i); SBase_unsetNotes((SBase_t*)sp); } for(i=0; i < Model_getNumUnitDefinitions(m); i++) { UnitDefinition_t* sp = Model_getUnitDefinition(m, i); SBase_unsetNotes((SBase_t*)sp); } for(i=0; i < Model_getNumParameters(m); i++) { Parameter_t* sp = Model_getParameter(m, i); SBase_unsetNotes((SBase_t*)sp); } for(i=0; i < Model_getNumRules(m); i++) { Rule_t* sp = Model_getRule(m, i); SBase_unsetNotes((SBase_t*)sp); } for(i=0; i < Model_getNumInitialAssignments(m); i++) { InitialAssignment_t* sp = Model_getInitialAssignment(m, i); SBase_unsetNotes((SBase_t*)sp); } for(i=0; i < Model_getNumEvents(m); i++) { Event_t* sp = Model_getEvent(m, i); SBase_unsetNotes((SBase_t*)sp); for(j=0; j < Event_getNumEventAssignments(sp); j++) { EventAssignment_t* ea = Event_getEventAssignment(sp, j); SBase_unsetNotes((SBase_t*)ea); } } for(i=0; i < Model_getNumSpeciesTypes(m); i++) { SpeciesType_t* sp = Model_getSpeciesType(m, i); SBase_unsetNotes((SBase_t*)sp); } for(i=0; i < Model_getNumConstraints(m); i++) { Constraint_t* sp = Model_getConstraint(m, i); SBase_unsetNotes((SBase_t*)sp); } writeSBML(document, argv[2]); SBMLDocument_free(document); return errors; }
int main (int argc, char* argv[]) { unsigned int i,j,errors; const char* filename; SBMLDocument_t* document; Model_t* m; if (argc != 2) { printf("\nUsage: printNotes filename\n\n"); return 1; } filename = argv[1]; document = readSBML(filename); errors = SBMLDocument_getNumErrors( document); printf("\n%s\n\n", filename); if(errors > 0) { SBMLDocument_printErrors(document, stderr); SBMLDocument_free(document); return errors; } /* Model */ m = SBMLDocument_getModel(document); printNotes((SBase_t*)m, Model_getId(m)); for(i=0; i < Model_getNumReactions(m); i++) { Reaction_t* re = Model_getReaction( m, i); printNotes((SBase_t*)re, Reaction_getId(re)); /* SpeciesReference (Reactant) */ for(j=0; j < Reaction_getNumReactants( re); j++) { SpeciesReference_t* rt = Reaction_getReactant(re, j); if (SBase_isSetNotes((SBase_t*) rt)) printf(" "); printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) ); } /* SpeciesReference (Product) */ for(j=0; j < Reaction_getNumProducts( re ); j++) { SpeciesReference_t* rt = Reaction_getProduct( re, j); if (SBase_isSetNotes((SBase_t*) rt)) printf(" "); printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) ); } /* ModifierSpeciesReference (Modifiers) */ for(j=0; j < Reaction_getNumModifiers( re ); j++) { SpeciesReference_t* md = Reaction_getModifier(re, j); if (SBase_isSetNotes((SBase_t*) md)) printf(" "); printNotes((SBase_t*)md, SpeciesReference_getSpecies( md ) ); } /* KineticLaw */ if(Reaction_isSetKineticLaw( re )) { KineticLaw_t* kl = Reaction_getKineticLaw( re ); if (SBase_isSetNotes((SBase_t*) kl)) printf(" "); printNotes((SBase_t*)kl, ""); /* Parameter */ for(j=0; j < KineticLaw_getNumParameters( kl ); j++) { Parameter_t* pa = KineticLaw_getParameter( kl, j); if (SBase_isSetNotes((SBase_t*) pa)) printf(" "); printNotes((SBase_t*)pa, Parameter_getId(pa)); } } } /* Species */ for(i=0; i < Model_getNumSpecies(m); i++) { Species_t* sp = Model_getSpecies(m, i); printNotes((SBase_t*)sp, Species_getId(sp)); } /* Compartments */ for(i=0; i < Model_getNumCompartments( m ); i++) { Compartment_t* sp = Model_getCompartment(m, i); printNotes((SBase_t*)sp, Compartment_getId(sp)); } /* FunctionDefinition */ for(i=0; i < Model_getNumFunctionDefinitions(m); i++) { FunctionDefinition_t* sp = Model_getFunctionDefinition(m, i); printNotes((SBase_t*)sp, FunctionDefinition_getId(sp)); } /* UnitDefinition */ for(i=0; i < Model_getNumUnitDefinitions(m); i++) { UnitDefinition_t* sp = Model_getUnitDefinition( m, i); printNotes((SBase_t*)sp, UnitDefinition_getId(sp)); } /* Parameter */ for(i=0; i < Model_getNumParameters( m ); i++) { Parameter_t* sp = Model_getParameter( m, i); printNotes((SBase_t*)sp, Parameter_getId(sp)); } /* Rule */ for(i=0; i < Model_getNumReactions( m ); i++) { Rule_t* sp = Model_getRule(m, i); printNotes((SBase_t*)sp, ""); } /* InitialAssignment */ for(i=0; i < Model_getNumInitialAssignments(m); i++) { InitialAssignment_t* sp = Model_getInitialAssignment(m, i); printNotes((SBase_t*)sp, ""); } /* Event */ for(i=0; i < Model_getNumEvents(m); i++) { Event_t* sp = Model_getEvent(m, i); printNotes((SBase_t*)sp, Event_getId(sp)); /* Trigger */ if(Event_isSetTrigger( sp )) { Trigger_t* tg = Event_getTrigger(sp); if (SBase_isSetNotes( (SBase_t*) tg)) printf( " " ); printNotes((SBase_t*)tg, ""); } /* Delay */ if(Event_isSetDelay(sp)) { Delay_t* dl = Event_getDelay(sp); if (SBase_isSetNotes( (SBase_t*) dl)) printf( " " ); printNotes((SBase_t*) dl, ""); } /* EventAssignment */ for(j=0; j < Event_getNumEventAssignments(sp); j++) { EventAssignment_t* ea = Event_getEventAssignment(sp, j); if (SBase_isSetNotes( (SBase_t*) ea)) printf( " " ); printNotes((SBase_t*)ea, ""); } } /* SpeciesType */ for(i=0; i < Model_getNumSpeciesTypes(m); i++) { SpeciesType_t* sp = Model_getSpeciesType(m, i); printNotes((SBase_t*)sp, SpeciesType_getId(sp)); } /* Constraints */ for(i=0; i < Model_getNumConstraints(m); i++) { Constraint_t* sp = Model_getConstraint(m, i); printNotes((SBase_t*)sp, ""); } SBMLDocument_free( document ); return errors; }
void printReactions(Model_t *m, FILE *f) { int i,j,k; Reaction_t *r; SpeciesReference_t *sref; KineticLaw_t *kl; Rule_t *rl; AssignmentRule_t *asr; AlgebraicRule_t *alr; RateRule_t *rr; Event_t *e; EventAssignment_t *ea; Parameter_t *p; FunctionDefinition_t *fd; SBMLTypeCode_t type; const ASTNode_t *math; math = NULL; fprintf(f, "\n"); for(i=0;i<Model_getNumParameters(m);i++){ if(i==0) fprintf(f, "# Global parameters:\n"); p = Model_getParameter(m,i); if(Parameter_isSetId(p)) fprintf(f, "%s ", Parameter_getId(p)); if(Parameter_isSetName(p)) fprintf(f, "(%s) ", Parameter_getName(p)); if(Parameter_isSetValue(p)) fprintf(f, "= %g; ", Parameter_getValue(p)); if(Parameter_isSetUnits(p)) fprintf(f, "[%s]; ", Parameter_getUnits(p)); if(!Parameter_getConstant(p)) fprintf(f, "(variable);"); fprintf(f, "\n"); if ( i==Model_getNumParameters(m)-1 ) fprintf(f, "\n"); } fprintf(f, "# Reactions:\n"); for ( i=0; i<Model_getNumReactions(m); i++ ) { r = Model_getReaction(m,i); fprintf(f, "%s: %s", Reaction_isSetName(r) ? Reaction_getName(r) : Reaction_getId(r), Reaction_getFast(r) ? "(fast)" : ""); for ( k=0; k<Reaction_getNumReactants(r); k++ ) { sref = Reaction_getReactant(r,k); if ( SpeciesReference_isSetStoichiometryMath(sref) ) fprintf(f, "%s ", SBML_formulaToString(\ SpeciesReference_getStoichiometryMath(sref))); else if ( SpeciesReference_getStoichiometry(sref) != 1. ) fprintf(f, "%g ", SpeciesReference_getStoichiometry(sref)); fprintf(f, "%s", SpeciesReference_getSpecies(sref)); if(k+1<Reaction_getNumReactants(r)) fprintf(f, "%s", " + "); } fprintf(f, "%s", Reaction_getReversible(r) ? " <-> " : " -> "); for ( k=0; k<Reaction_getNumProducts(r); k++ ) { sref = Reaction_getProduct(r,k); if ( SpeciesReference_isSetStoichiometryMath(sref) ) fprintf(f, "%s ", SBML_formulaToString(\ SpeciesReference_getStoichiometryMath(sref))); else if ( SpeciesReference_getStoichiometry(sref) != 1. ) fprintf(f, "%g ", SpeciesReference_getStoichiometry(sref)); fprintf(f, "%s", SpeciesReference_getSpecies(sref)); if(k+1<Reaction_getNumProducts(r)) fprintf(f, "%s", " + "); } fprintf(f, "; "); if(Reaction_isSetKineticLaw(r)){ kl = Reaction_getKineticLaw(r); math = KineticLaw_getMath(kl); fprintf(f, "%s;", SBML_formulaToString(math)); for(k=0;k<KineticLaw_getNumParameters(kl);k++){ p = KineticLaw_getParameter(kl,k); fprintf(f, " %s", Parameter_getId(p)); if(Parameter_isSetName(p)) fprintf(f, " (%s)", Parameter_getName(p)); if(Parameter_isSetValue(p)) fprintf(f, " = %g", Parameter_getValue(p)); if(Parameter_isSetUnits(p)) fprintf(f, " [%s]", Parameter_getUnits(p)); if ( !Parameter_getConstant(p) ) fprintf(f, " (variable)"); fprintf(f, ";"); } /* fprintf(f, "\n"); */ }else fprintf(f, "# no rate law is set for this reaction."); fprintf(f, "\n"); } for(i=0;i<Model_getNumRules(m);i++){ rl = Model_getRule(m,i); if ( i == 0 ) { fprintf(f, "# Rules:\n"); } type = SBase_getTypeCode((SBase_t *)rl); if ( type == SBML_RATE_RULE ) { rr = (RateRule_t *) rl; fprintf(f, " rateRule: d%s/dt = ", RateRule_getVariable(rr)); } if ( type == SBML_ALGEBRAIC_RULE ) { alr = (AlgebraicRule_t *) rl; fprintf(f, " algebraicRule: 0 = "); } if ( type == SBML_ASSIGNMENT_RULE ) { asr = (AssignmentRule_t *) rl; fprintf(f, " assignmentRule (%s): %s = ", RuleType_toString(AssignmentRule_getType(asr)), AssignmentRule_getVariable(asr)); } if(!Rule_isSetMath(rl)){ if(Rule_isSetFormula(rl)){ Rule_setMathFromFormula(rl); } } if(Rule_isSetMath(rl)) fprintf(f, "%s\n", SBML_formulaToString(Rule_getMath(rl))); } fprintf(f, "\n"); for(i=0;i<Model_getNumEvents(m);i++){ if(i==0) fprintf(f, "# Events:\n"); e = Model_getEvent(m,i); if(Event_isSetId(e)) fprintf(f, "%s: ", Event_getId(e)); if(Event_isSetName(e)) fprintf(f, "(%s) ", Event_getName(e)); if(Event_isSetTrigger(e)) { math = Event_getTrigger(e); fprintf(f, "trigger: %s\n", SBML_formulaToString(math)); } if(Event_isSetDelay(e)) fprintf(f, "delay: %s;\n", SBML_formulaToString(Event_getDelay(e))); if(Event_isSetTimeUnits(e)) fprintf(f, "time Units: %s;\n", Event_getTimeUnits(e)); for(k=0;k<Event_getNumEventAssignments(e);k++){ ea = Event_getEventAssignment(e,k); if(EventAssignment_isSetVariable(ea)) fprintf(f, " event: %s = %s;\n", EventAssignment_getVariable(ea), EventAssignment_isSetMath(ea) ? SBML_formulaToString(EventAssignment_getMath(ea)) : "# no math set;\n"); } if(i==Model_getNumEvents(m)-1) fprintf(f, "\n"); } for ( i=0; i<Model_getNumFunctionDefinitions(m); i++ ) { if ( i==0 ) fprintf(f, "# Functions:\n"); fd = Model_getFunctionDefinition(m,i); if ( FunctionDefinition_isSetName(fd) ) fprintf(f, "%s: ", FunctionDefinition_getName(fd)); if(FunctionDefinition_isSetId(fd) && FunctionDefinition_isSetMath(fd)){ fprintf(f, "%s( ", FunctionDefinition_getId(fd)); math = FunctionDefinition_getMath(fd); for(j=0;j<ASTNode_getNumChildren(math)-1;j++){ fprintf(f, "%s", SBML_formulaToString(ASTNode_getChild(math, j))); if(j<ASTNode_getNumChildren(math)-2) fprintf(f, ", "); if(j==ASTNode_getNumChildren(math)-2) fprintf(f, ") = "); } fprintf(f, "%s;", SBML_formulaToString(ASTNode_getRightChild(math))); } fprintf(f, "\n"); } }