END_TEST START_TEST (test_Reaction_setName) { const char *name = "MapK_Cascade"; Reaction_setName(R, name); fail_unless( !strcmp(Reaction_getName(R), name) ); fail_unless( Reaction_isSetName(R) ); if (Reaction_getName(R) == name) { fail("Reaction_setName(...) did not make a copy of string."); } /* Reflexive case (pathological) */ Reaction_setName(R, Reaction_getName(R)); fail_unless( !strcmp(Reaction_getName(R), name) ); Reaction_setName(R, NULL); fail_unless( !Reaction_isSetName(R) ); if (Reaction_getName(R) != NULL) { fail("Reaction_setName(R, NULL) did not clear string."); } }
END_TEST START_TEST (test_Reaction_setName1) { int i = Reaction_setName(R, "cell"); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( Reaction_isSetName(R) ); i = Reaction_unsetName(R); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( !Reaction_isSetName(R) ); }
END_TEST START_TEST (test_Reaction_setName2) { Reaction_t *p = Reaction_create(2, 2); int i = Reaction_setName(p, "1cell"); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( Reaction_isSetName(p) ); i = Reaction_unsetName(p); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( !Reaction_isSetName(p) ); Reaction_free(p); }
static int drawModelTxt(Model_t *m, char *file) { Species_t *s; Reaction_t *re; const ASTNode_t *math; SpeciesReference_t *sref; ModifierSpeciesReference_t *mref; int i,j; int reversible; char filename[WORDSIZE]; FILE *f; sprintf(filename, "%s.dot", file); f = fopen(filename, "w"); fprintf(f ,"digraph reactionnetwork {\n"); fprintf(f ,"label=\"%s\";\n", Model_isSetName(m) ? Model_getName(m) : (Model_isSetId(m) ? Model_getId(m) : "noId") ); fprintf(f ,"overlap=scale;\n"); for ( i=0; i<Model_getNumReactions(m); i++ ) { re = Model_getReaction(m,i); reversible = Reaction_getReversible(re); for ( j=0; j<Reaction_getNumModifiers(re); j++ ) { mref = Reaction_getModifier(re,j); fprintf(f ,"%s->%s [style=dashed arrowhead=odot];\n", ModifierSpeciesReference_getSpecies(mref), Reaction_getId(re)); } for ( j=0; j<Reaction_getNumReactants(re); j++ ) { sref = Reaction_getReactant(re,j); fprintf(f ,"%s->%s [label=\"", SpeciesReference_getSpecies(sref), Reaction_getId(re)); if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) { math = SpeciesReference_getStoichiometryMath(sref); if ( (strcmp(SBML_formulaToString(math),"1") != 0) ) { fprintf(f ,"%s", SBML_formulaToString(math)); } } else { if ( SpeciesReference_getStoichiometry(sref) != 1) { fprintf(f ,"%g",SpeciesReference_getStoichiometry(sref)); } } if ( reversible == 1 ) { fprintf(f ,"\" arrowtail=onormal];\n"); } else { fprintf(f ,"\" ];\n"); } } for ( j=0; j<Reaction_getNumProducts(re); j++ ) { sref = Reaction_getProduct(re,j); fprintf(f ,"%s->%s [label=\"", Reaction_getId(re), SpeciesReference_getSpecies(sref)); if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) { math = SpeciesReference_getStoichiometryMath(sref); if ( (strcmp(SBML_formulaToString(math),"1") != 0) ) { fprintf(f ,"%s ", SBML_formulaToString(math)); } } else { if ( SpeciesReference_getStoichiometry(sref) != 1) { fprintf(f ,"%g ",SpeciesReference_getStoichiometry(sref)); } } if ( reversible == 1 ) { fprintf(f ,"\" arrowtail=onormal];\n"); } else { fprintf(f ,"\" ];\n"); } } } for ( i=0; i<Model_getNumReactions(m); i++ ) { re = Model_getReaction(m,i); fprintf(f ,"%s [label=\"%s\" shape=box];\n", Reaction_getId(re), Reaction_isSetName(re) ? Reaction_getName(re) : Reaction_getId(re)); } for ( i=0; i<Model_getNumSpecies(m); i++) { s = Model_getSpecies(m, i); fprintf(f ,"%s [label=\"%s\"];", Species_getId(s), Species_isSetName(s) ? Species_getName(s) : Species_getId(s)); } fprintf(f ,"}\n"); return 1; }
SBML_ODESOLVER_API int drawModel(Model_t *m, char* file, char *format) { #if !USE_GRAPHVIZ SolverError_error( WARNING_ERROR_TYPE, SOLVER_ERROR_NO_GRAPHVIZ, "odeSolver has been compiled without GRAPHIZ functionality. ", "Graphs are printed to stdout in the graphviz' .dot format."); drawModelTxt(m, file); #else GVC_t *gvc; Agraph_t *g; Agnode_t *r; Agnode_t *s; Agedge_t *e; Agsym_t *a; Species_t *sp; Reaction_t *re; const ASTNode_t *math; SpeciesReference_t *sref; ModifierSpeciesReference_t *mref; char *output[4]; char *command = "dot"; char *formatopt; char *outfile; int i,j; int reversible; char name[WORDSIZE]; char label[WORDSIZE]; /* setting name of outfile */ ASSIGN_NEW_MEMORY_BLOCK(outfile, strlen(file)+ strlen(format)+7, char, 0); sprintf(outfile, "-o%s_rn.%s", file, format); /* setting output format */ ASSIGN_NEW_MEMORY_BLOCK(formatopt, strlen(format)+3, char, 0); sprintf(formatopt, "-T%s", format); /* construct command-line */ output[0] = command; output[1] = formatopt; output[2] = outfile; output[3] = NULL; /* set up renderer context */ gvc = (GVC_t *) gvContext(); #if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION < 4 dotneato_initialize(gvc, 3, output); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4 parse_args(gvc, 3, output); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3 gvParseArgs(gvc, 3, output); #endif g = agopen("G", AGDIGRAPH); /* avoid overlapping nodes, for graph embedding by neato */ a = agraphattr(g, "overlap", ""); agxset(g, a->index, "scale"); for ( i=0; i<Model_getNumReactions(m); i++ ) { re = Model_getReaction(m,i); reversible = Reaction_getReversible(re); sprintf(name, "%s", Reaction_getId(re)); r = agnode(g,name); a = agnodeattr(g, "shape", "ellipse"); agxset(r, a->index, "box"); sprintf(label, "%s", Reaction_isSetName(re) ? Reaction_getName(re) : Reaction_getId(re)); agset(r, "label", label); sprintf(label, "%s.htm", Reaction_getId(re)); a = agnodeattr(g, "URL", ""); agxset(r, a->index, label); for ( j=0; j<Reaction_getNumModifiers(re); j++ ) { mref = Reaction_getModifier(re,j); sp = Model_getSpeciesById(m, ModifierSpeciesReference_getSpecies(mref)); sprintf(name,"%s", Species_getId(sp)); s = agnode(g,name); sprintf(label, "%s", Species_isSetName(sp) ? Species_getName(sp) : Species_getId(sp)); agset(s, "label", label); if ( Species_getBoundaryCondition(sp) ) { a = agnodeattr(g, "color", ""); agxset(s, a->index, "blue"); } if ( Species_getConstant(sp) ) { a = agnodeattr(g, "color", ""); agxset(s, a->index, "green4"); } sprintf(label, "%s.htm", Species_getId(sp)); a = agnodeattr(g, "URL", ""); agxset(s, a->index, label); e = agedge(g,s,r); a = agedgeattr(g, "style", ""); agxset(e, a->index, "dashed"); a = agedgeattr(g, "arrowhead", ""); agxset(e, a->index, "odot"); } for ( j=0; j<Reaction_getNumReactants(re); j++ ) { sref = Reaction_getReactant(re,j); sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref)); sprintf(name,"%s", Species_getId(sp)); s = agnode(g, name); sprintf(label, "%s", Species_isSetName(sp) ? Species_getName(sp) : Species_getId(sp)); agset(s, "label", label); if ( Species_getBoundaryCondition(sp) ) { a = agnodeattr(g, "color", ""); agxset(s, a->index, "blue"); } if ( Species_getConstant(sp) ) { a = agnodeattr(g, "color", ""); agxset(s, a->index, "green4"); } sprintf(label, "%s.htm", Species_getId(sp)); a = agnodeattr(g, "URL", ""); agxset(s, a->index, label); e = agedge(g,s,r); a = agedgeattr(g, "label", ""); if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) { math = SpeciesReference_getStoichiometryMath(sref); if ( (strcmp(SBML_formulaToString(math),"1") != 0) ) { agxset (e, a->index, SBML_formulaToString(math)); } } else { if ( SpeciesReference_getStoichiometry(sref) != 1 ) { sprintf(name, "%g", SpeciesReference_getStoichiometry(sref)); agxset (e, a->index, name); } } if ( reversible == 1 ) { a = agedgeattr(g, "arrowtail", ""); agxset(e, a->index, "onormal"); } } for ( j=0; j<Reaction_getNumProducts(re); j++ ) { sref = Reaction_getProduct(re,j); sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref)); sprintf(name,"%s", Species_getId(sp)); s = agnode(g,name); sprintf(label, "%s", Species_isSetName(sp) ? Species_getName(sp) : Species_getId(sp)); agset(s, "label", label); if ( Species_getBoundaryCondition(sp) ) { a = agnodeattr(g, "color", ""); agxset(s, a->index, "blue"); } if ( Species_getConstant(sp) ) { a = agnodeattr(g, "color", ""); agxset(s, a->index, "green4"); } sprintf(label, "%s.htm", Species_getId(sp)); a = agnodeattr(g, "URL", ""); agxset(s, a->index, label); e = agedge(g,r,s); a = agedgeattr(g, "label", ""); if ( SpeciesReference_isSetStoichiometryMath(sref) ) { math = SpeciesReference_getStoichiometryMath(sref); if ( (strcmp(SBML_formulaToString(math),"1") != 0) ) { agxset (e, a->index, SBML_formulaToString(math)); } } else { if ( SpeciesReference_getStoichiometry(sref) != 1 ) { sprintf(name, "%g",SpeciesReference_getStoichiometry(sref)); agxset (e, a->index,name); } } if ( reversible == 1 ) { a = agedgeattr(g, "arrowtail", ""); agxset(e, a->index, "onormal"); } } } /* Compute a layout */ #if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2 gvBindContext(gvc, g); dot_layout(g); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4 gvlayout_layout(gvc, g); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3 gvLayoutJobs(gvc, g); #endif /* Write the graph according to -T and -o options */ #if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2 dotneato_write(gvc); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4 emit_jobs(gvc, g); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3 gvRenderJobs(gvc, g); #endif /* Clean out layout data */ #if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2 dot_cleanup(g); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4 gvlayout_cleanup(gvc, g); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3 gvFreeLayout(gvc, g); #endif /* Free graph structures */ #if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2 dot_cleanup(g); #else agclose(g); #endif /* Clean up output file and errors */ #if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2 gvFREEcontext(gvc); dotneato_eof(gvc); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4 dotneato_terminate(gvc); #elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3 gvFreeContext(gvc); #endif xfree(formatopt); xfree(outfile); #endif return 1; }
static int printXMGReactionTimeCourse ( cvodeData_t *data ) { int i, j, k, n; double maxY, minY, result; Model_t *m; Reaction_t *r; KineticLaw_t *kl; ASTNode_t **kls; odeModel_t *om = data->model; cvodeResults_t *results = data->results; maxY = 0.0; minY = 0.0; fprintf(stderr, "Printing time development of reaction fluxes to XMGrace!\n"); if ( om->m == NULL ) { fprintf(stderr, "Error: No reaction model availabe\n"); return 1; } else m = om->m; if ( openXMGrace(data) > 0 ) { fprintf(stderr, "Error: Couldn't open XMGrace\n"); return 1; } GracePrintf("yaxis label \"%s\"", "flux [substance/time]"); if ( Model_isSetName(m) ) GracePrintf("subtitle \"%s, %s\"", Model_getName(m), "reaction flux time courses"); else if ( Model_isSetId(m) ) GracePrintf("subtitle \"%s, %s\"", Model_getId(m), "reaction flux time courses"); else GracePrintf("subtitle \"model has no name, %s/id\"", "reaction flux time courses"); /* print legend */ for ( i=0; i<Model_getNumReactions(m); i++ ) { r = Model_getReaction(m, i); if ( Reaction_isSetName(r) ) GracePrintf("g0.s%d legend \"%s: %s \"\n", i+1, Reaction_getId(r), Reaction_getName(r)); else GracePrintf("g0.s%d legend \"%s \"\n", i+1, Reaction_getId(r)); } GracePrintf("legend 1.155, 0.85"); GracePrintf("legend font 8"); GracePrintf("legend char size 0.6"); if(!(kls = (ASTNode_t **)calloc(Model_getNumReactions(m), sizeof(ASTNode_t *)))) fprintf(stderr, "failed!\n"); for ( i=0; i<Model_getNumReactions(m); i++ ) { r = Model_getReaction(m, i); kl = Reaction_getKineticLaw(r); kls[i] = copyAST(KineticLaw_getMath(kl)); AST_replaceNameByParameters(kls[i], KineticLaw_getListOfParameters(kl)); AST_replaceConstants(m, kls[i]); } /* evaluate flux for each time point and print to XMGrace */ for ( i=0; i<=results->nout; i++ ) { n = 1; /* set time and variable values to values at time[k] */ data->currenttime = results->time[i]; for ( j=0; j<data->model->neq; j++ ) data->value[j] = results->value[j][i]; /* evaluate kinetic law expressions */ for ( j=0; j<Model_getNumReactions(m); j++ ) { result = evaluateAST(kls[j], data); if ( result > maxY ) { maxY = result; GracePrintf("world ymax %g", 1.25*maxY); } if ( result < minY ) { minY = result; GracePrintf("world ymin %g", 1.25*minY); } GracePrintf("g0.s%d point %g, %g", n, results->time[i], result); n++; } } GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10); GracePrintf("redraw"); closeXMGrace(data, "flux"); /* free temporary ASTNodes */ for ( i=0; i<Model_getNumReactions(m); i++ ) ASTNode_free(kls[i]); free(kls); return 0; }
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"); } }