END_TEST START_TEST(test_parseModel_repressilator) { doc = parseModel(EXAMPLES_FILENAME("repressilator.xml"), 0, 1); ck_assert(doc != NULL); model = SBMLDocument_getModel(doc); ck_assert(model != NULL); ck_assert(Model_getNumFunctionDefinitions(model) == 0); ck_assert(Model_getNumUnitDefinitions(model) == 0); ck_assert(Model_getNumCompartmentTypes(model) == 0); ck_assert(Model_getNumSpeciesTypes(model) == 0); ck_assert(Model_getNumCompartments(model) == 1); ck_assert(Model_getNumSpecies(model) == 6); ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0); ck_assert(Model_getNumParameters(model) == 3); ck_assert(Model_getNumInitialAssignments(model) == 0); ck_assert(Model_getNumRules(model) == 6); ck_assert(Model_getNumConstraints(model) == 0); ck_assert(Model_getNumReactions(model) == 0); ck_assert(Model_getNumEvents(model) == 0); CHECK_PARAMETER(model, 0, "alpha"); CHECK_PARAMETER(model, 1, "beta"); CHECK_PARAMETER(model, 2, "rho"); CHECK_RULE(model, 0, "beta * (y1 - x1)"); CHECK_RULE(model, 1, "beta * (y2 - x2)"); CHECK_RULE(model, 2, "beta * (y3 - x3)"); CHECK_RULE(model, 3, "alpha * x1 / (1 + x1 + rho * x3) - y1"); CHECK_RULE(model, 4, "alpha * x2 / (1 + x2 + rho * x1) - y2"); CHECK_RULE(model, 5, "alpha * x3 / (1 + x3 + rho * x2) - y3"); }
END_TEST START_TEST(test_parseModel_basic) { doc = parseModel(EXAMPLES_FILENAME("basic.xml"), 0, 1); ck_assert(doc != NULL); model = SBMLDocument_getModel(doc); ck_assert(model != NULL); ck_assert(Model_getNumFunctionDefinitions(model) == 0); ck_assert(Model_getNumUnitDefinitions(model) == 0); ck_assert(Model_getNumCompartmentTypes(model) == 0); ck_assert(Model_getNumSpeciesTypes(model) == 0); ck_assert(Model_getNumCompartments(model) == 1); ck_assert(Model_getNumSpecies(model) == 2); ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0); ck_assert(Model_getNumParameters(model) == 1); ck_assert(Model_getNumInitialAssignments(model) == 0); ck_assert(Model_getNumRules(model) == 0); ck_assert(Model_getNumConstraints(model) == 0); ck_assert(Model_getNumReactions(model) == 2); ck_assert(Model_getNumEvents(model) == 0); CHECK_PARAMETER(model, 0, "k_1"); CHECK_REACTION(model, 0, "R1", "k_1 * S1"); CHECK_REACTION(model, 1, "R2", "k_2 * S2"); }
void printMath (Model_t *m) { unsigned int n; for (n = 0; n < Model_getNumFunctionDefinitions(m); ++n) { printFunctionDefinition(n + 1, Model_getFunctionDefinition(m, n)); } for (n = 0; n < Model_getNumRules(m); ++n) { printRuleMath(n + 1, Model_getRule(m, n)); } printf("\n"); for (n = 0; n < Model_getNumReactions(m); ++n) { printReactionMath(n + 1, Model_getReaction(m, n)); } printf("\n"); for (n = 0; n < Model_getNumEvents(m); ++n) { printEventMath(n + 1, Model_getEvent(m, n)); } }
int main (int argc, char *argv[]) { const char *filename; SBMLDocument_t *d; Model_t *m; unsigned int level, version; if (argc != 2) { printf("Usage: printSBML filename\n"); return 2; } filename = argv[1]; d = readSBML(filename); SBMLDocument_printErrors(d, stdout); m = SBMLDocument_getModel(d); level = SBMLDocument_getLevel (d); version = SBMLDocument_getVersion(d); printf("\n"); printf("File: %s (Level %u, version %u)\n", filename, level, version); if (m == NULL) { printf("No model present."); return 1; } printf(" "); printf(" model id: %s\n", Model_isSetId(m) ? Model_getId(m) : "(empty)"); printf( "functionDefinitions: %d\n", Model_getNumFunctionDefinitions(m) ); printf( " unitDefinitions: %d\n", Model_getNumUnitDefinitions (m) ); printf( " compartmentTypes: %d\n", Model_getNumCompartmentTypes (m) ); printf( " specieTypes: %d\n", Model_getNumSpeciesTypes (m) ); printf( " compartments: %d\n", Model_getNumCompartments (m) ); printf( " species: %d\n", Model_getNumSpecies (m) ); printf( " parameters: %d\n", Model_getNumParameters (m) ); printf( " initialAssignments: %d\n", Model_getNumInitialAssignments (m) ); printf( " rules: %d\n", Model_getNumRules (m) ); printf( " constraints: %d\n", Model_getNumConstraints (m) ); printf( " reactions: %d\n", Model_getNumReactions (m) ); printf( " events: %d\n", Model_getNumEvents (m) ); printf( "\n" ); SBMLDocument_free(d); return 0; }
void printModel(Model_t *m, FILE *f) { fprintf(f, "\n"); fprintf(f, "Model Statistics:\n"); fprintf(f, " Model id: %s\n", Model_isSetId(m) ? Model_getId(m) : "(not set)"); fprintf(f, " Model name: %s\n", Model_isSetName(m) ? Model_getName(m) : "(not set)"); fprintf(f, "\n"); fprintf(f, " Compartments: %d\n", Model_getNumCompartments(m)); fprintf(f, " Species: %d\n", Model_getNumSpecies(m)); fprintf(f, " Reactions: %d\n", Model_getNumReactions(m)); fprintf(f, " Rules: %d\n", Model_getNumRules(m)); fprintf(f, " Events: %d\n", Model_getNumEvents(m)); fprintf(f, " Functions: %d\n", Model_getNumFunctionDefinitions(m) ); fprintf(f, "\n"); }
void printMath (Model_t *m) { unsigned int n; /* a digraph must have a name thus * need to check that Model_getId does not return NULL * and provide a name if it does */ if (Model_getId(m) != NULL) { fprintf(fout, "digraph %s {\n", Model_getId(m)); } else { fprintf(fout, "digraph example {\n"); } fprintf(fout, "compound=true;\n"); for (n = 0; n < Model_getNumFunctionDefinitions(m); ++n) { printFunctionDefinition(n + 1, Model_getFunctionDefinition(m, n)); } for (n = 0; n < Model_getNumRules(m); ++n) { printRuleMath(n + 1, Model_getRule(m, n)); } printf("\n"); for (n = 0; n < Model_getNumReactions(m); ++n) { printReactionMath(n + 1, Model_getReaction(m, n)); } printf("\n"); for (n = 0; n < Model_getNumEvents(m); ++n) { printEventMath(n + 1, Model_getEvent(m, n)); } fprintf(fout, "}\n"); }
END_TEST START_TEST(test_parseModel_huang96) { doc = parseModel(EXAMPLES_FILENAME("huang96.xml"), 0, 1); ck_assert(doc != NULL); model = SBMLDocument_getModel(doc); ck_assert(model != NULL); ck_assert(Model_getNumFunctionDefinitions(model) == 0); ck_assert(Model_getNumUnitDefinitions(model) == 0); ck_assert(Model_getNumCompartmentTypes(model) == 0); ck_assert(Model_getNumSpeciesTypes(model) == 0); ck_assert(Model_getNumCompartments(model) == 1); ck_assert(Model_getNumSpecies(model) == 22); ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0); ck_assert(Model_getNumParameters(model) == 0); ck_assert(Model_getNumInitialAssignments(model) == 0); ck_assert(Model_getNumRules(model) == 0); ck_assert(Model_getNumConstraints(model) == 0); ck_assert(Model_getNumReactions(model) == 20); ck_assert(Model_getNumEvents(model) == 0); CHECK_REACTION(model, 0, "r1a", "a1 * E1 * KKK - d1 * E1_KKK"); CHECK_REACTION(model, 1, "r1b", "k2 * E1_KKK"); CHECK_REACTION(model, 2, "r2a", "a2 * E2 * P_KKK - d2 * E2_P_KKK"); CHECK_REACTION(model, 3, "r2b", "k2 * E2_P_KKK"); CHECK_REACTION(model, 4, "r3a", "a3 * KK * P_KKK - d3 * P_KKK_KK"); CHECK_REACTION(model, 5, "r3b", "k3 * P_KKK_KK"); CHECK_REACTION(model, 6, "r4a", "a4 * P_KK * KKPase - d4 * KKPase_P_KK"); CHECK_REACTION(model, 7, "r4b", "k4 * KKPase_P_KK"); CHECK_REACTION(model, 8, "r5a", "a5 * P_KK * P_KKK - d5 * P_KKK_P_KK"); CHECK_REACTION(model, 9, "r5b", "k5 * P_KKK_P_KK"); CHECK_REACTION(model, 10, "r6a", "a6 * PP_KK * KKPase - d6 * KKPase_PP_KK"); CHECK_REACTION(model, 11, "r6b", "k6 * KKPase_PP_KK"); CHECK_REACTION(model, 12, "r7a", "a7 * K * PP_KK - d7 * PP_KK_K"); CHECK_REACTION(model, 13, "r7b", "k7 * PP_KK_K"); CHECK_REACTION(model, 14, "r8a", "a8 * P_K * KPase - d8 * KPase_P_K"); CHECK_REACTION(model, 15, "r8b", "k8 * KPase_P_K"); CHECK_REACTION(model, 16, "r9a", "a9 * P_K * PP_KK - d9 * PP_KK_P_K"); CHECK_REACTION(model, 17, "r9b", "k9 * PP_KK_P_K"); CHECK_REACTION(model, 18, "r10a", "a10 * PP_K * KPase - d10 * KPase_PP_K"); CHECK_REACTION(model, 19, "r10b", "k10 * KPase_PP_K"); /* TODO */ }
END_TEST START_TEST(test_parseModel_events_1_event_1_assignment_l2) { doc = parseModel(EXAMPLES_FILENAME("events-1-event-1-assignment-l2.xml"), 0, 1); ck_assert(doc != NULL); model = SBMLDocument_getModel(doc); ck_assert(model != NULL); ck_assert(Model_getNumFunctionDefinitions(model) == 0); ck_assert(Model_getNumUnitDefinitions(model) == 0); ck_assert(Model_getNumCompartmentTypes(model) == 0); ck_assert(Model_getNumSpeciesTypes(model) == 0); ck_assert(Model_getNumCompartments(model) == 1); ck_assert(Model_getNumSpecies(model) == 2); ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0); ck_assert(Model_getNumParameters(model) == 0); ck_assert(Model_getNumInitialAssignments(model) == 0); ck_assert(Model_getNumRules(model) == 0); ck_assert(Model_getNumConstraints(model) == 0); ck_assert(Model_getNumReactions(model) == 1); ck_assert(Model_getNumEvents(model) == 1); CHECK_REACTION(model, 0, "R", "S1"); /* TODO */ }
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"); } }
void ev_alter_tree_structure(Model_t *m, ASTNode_t **node_p, ASTNode_t *parent, int child_order, copied_AST *cp_AST){ ASTNode_t *zero_node; ASTNode_t *node, *next_node; ASTNode_t *pc_eq, *pc_cd, *times_node, *and_node, *not_node; unsigned int i, j; int p; ASTNode_t *arg_node_list[MAX_ARG_NUM]; unsigned int arg_node_num; FunctionDefinition_t *fd; ASTNode_t *fd_arg; ASTNode_t *fd_body; node = *node_p; for(i=0; i<ASTNode_getNumChildren(node); i++){ next_node = ASTNode_getChild(node, i); if(ASTNode_getNumChildren(node) == 1 && ASTNode_getType(node) == AST_MINUS){ zero_node = ASTNode_create(); ASTNode_setType(zero_node, AST_REAL); ASTNode_setReal(zero_node, 0); ASTNode_replaceChild(node, 0, zero_node); ASTNode_addChild(*node_p, next_node); }else{ ev_alter_tree_structure(m, &next_node, *node_p, i, cp_AST); } } if(ASTNode_getType(node) == AST_FUNCTION){ arg_node_num = ASTNode_getNumChildren(node); for(i=0; i<arg_node_num; i++){ arg_node_list[i] = ASTNode_getChild(node, i); } for(i=0; i<Model_getNumFunctionDefinitions(m); i++){ fd = (FunctionDefinition_t*)ListOf_get(Model_getListOfFunctionDefinitions(m), i); fd_body = (ASTNode_t*)FunctionDefinition_getBody(fd); if(strcmp(FunctionDefinition_getId(fd), ASTNode_getName(node)) == 0){ fd_body = ASTNode_deepCopy(fd_body); cp_AST->ast[cp_AST->num_of_copied_AST++] = fd_body; for(j=0; j<FunctionDefinition_getNumArguments(fd); j++){ fd_arg = (ASTNode_t*)FunctionDefinition_getArgument(fd, j); ASTNode_replaceArgument(fd_body, (char*)ASTNode_getName(fd_arg), arg_node_list[j]); } /* check_AST(fd_body, NULL); */ if(parent != NULL){ ASTNode_replaceChild(parent, child_order, fd_body); }else{ *node_p = fd_body; } node = *node_p; break; } } } if(ASTNode_getType(node) == AST_FUNCTION_PIECEWISE){ ASTNode_setType(node, AST_PLUS); ASTNode_setName(node, NULL); times_node = ASTNode_createWithType(AST_TIMES); pc_eq = ASTNode_getRightChild(node); ASTNode_addChild(times_node, pc_eq); if(ASTNode_getNumChildren(node) > 3){ and_node = ASTNode_createWithType(AST_LOGICAL_AND); ASTNode_addChild(times_node, and_node); for(p=(int)ASTNode_getNumChildren(node)-2; p >= 1; p = p-2){ pc_cd = ASTNode_getChild(node, p); not_node = ASTNode_createWithType(AST_LOGICAL_NOT); ASTNode_addChild(not_node, pc_cd); ASTNode_addChild(and_node, not_node); } ASTNode_reduceToBinary(and_node); }else{ pc_cd = ASTNode_getChild(node, 1); not_node = ASTNode_createWithType(AST_LOGICAL_NOT); ASTNode_addChild(not_node, pc_cd); ASTNode_addChild(times_node, not_node); } ASTNode_replaceChild(node, ASTNode_getNumChildren(node)-1, times_node); for(p=ASTNode_getNumChildren(node)-2; p >= 1; p = p-2){ times_node = ASTNode_createWithType(AST_TIMES); pc_eq = ASTNode_getChild(node, p-1); pc_cd = ASTNode_getChild(node, p); ASTNode_addChild(times_node, pc_eq); ASTNode_addChild(times_node, ASTNode_deepCopy(pc_cd)); ASTNode_removeChild(node, p); ASTNode_replaceChild(node ,p-1, times_node); } ASTNode_reduceToBinary(node); } return; }