END_TEST START_TEST (test_Reaction_addModifier1) { Reaction_t *m = Reaction_create(2, 2); SpeciesReference_t *p = SpeciesReference_createModifier(2, 2); SpeciesReference_t *p1 = SpeciesReference_createModifier(2, 2); SpeciesReference_setSpecies(p1, "k"); SpeciesReference_setId(p1, "k1"); int i = Reaction_addModifier(m, p); fail_unless( i == LIBSBML_INVALID_OBJECT); SpeciesReference_setSpecies(p, "k"); SpeciesReference_setId(p, "k1"); i = Reaction_addModifier(m, p); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( Reaction_getNumModifiers(m) == 1); i = Reaction_addModifier(m, p1); fail_unless( i == LIBSBML_DUPLICATE_OBJECT_ID); fail_unless( Reaction_getNumModifiers(m) == 1); SpeciesReference_free(p); SpeciesReference_free(p1); Reaction_free(m); }
END_TEST START_TEST (test_SBMLConvert_addModifiersToReaction) { SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2); Model_t *m = SBMLDocument_createModel(d); Reaction_t *r = Model_createReaction(m); KineticLaw_t *kl = Reaction_createKineticLaw(r); KineticLaw_setFormula(kl, "k1*S1*S2*S3*S4*S5"); SpeciesReference_t *ssr1; SpeciesReference_t *ssr2; Species_t *s1 = Model_createSpecies( m ); Species_setId( s1, "S1" ); Species_t *s2 = Model_createSpecies( m ); Species_setId( s2, "S2"); Species_t *s3 = Model_createSpecies( m ); Species_setId( s3, "S3"); Species_t *s4 = Model_createSpecies( m ); Species_setId( s4, "S4"); Species_t *s5 = Model_createSpecies( m ); Species_setId( s5, "S5"); SpeciesReference_t *sr1 = Reaction_createReactant( r ); SpeciesReference_t *sr2 = Reaction_createReactant( r ); SpeciesReference_t *sr3 = Reaction_createProduct ( r ); SpeciesReference_setSpecies(sr1, "S1"); SpeciesReference_setSpecies(sr2, "S2"); SpeciesReference_setSpecies(sr3, "S5"); fail_unless( Reaction_getNumModifiers(r) == 0, NULL ); fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 2, 1) == 1, NULL ); fail_unless( SBMLDocument_getLevel (d) == 2, NULL ); fail_unless( SBMLDocument_getVersion(d) == 1, NULL ); fail_unless( Reaction_getNumModifiers(Model_getReaction(m, 0)) == 2, NULL ); ssr1 = (SpeciesReference_t *) Reaction_getModifier(Model_getReaction(m, 0), 0); ssr2 = (SpeciesReference_t *) Reaction_getModifier(Model_getReaction(m, 0), 1); fail_unless( !strcmp(SpeciesReference_getSpecies(ssr1), "S3"), NULL ); fail_unless( !strcmp(SpeciesReference_getSpecies(ssr2), "S4"), NULL ); SBMLDocument_free(d); }
END_TEST START_TEST (test_Reaction_getProduct) { SpeciesReference_t *sr1 = SpeciesReference_create(2, 4); SpeciesReference_t *sr2 = SpeciesReference_create(2, 4); SpeciesReference_setSpecies(sr1, "P1"); SpeciesReference_setSpecies(sr2, "P2"); Reaction_addProduct(R, sr1); Reaction_addProduct(R, sr2); SpeciesReference_free(sr1); SpeciesReference_free(sr2); fail_unless( Reaction_getNumReactants(R) == 0 ); fail_unless( Reaction_getNumProducts (R) == 2 ); fail_unless( Reaction_getNumModifiers(R) == 0 ); sr1 = Reaction_getProduct(R, 0); sr2 = Reaction_getProduct(R, 1); fail_unless( !strcmp(SpeciesReference_getSpecies(sr1), "P1") ); fail_unless( !strcmp(SpeciesReference_getSpecies(sr2), "P2") ); }
END_TEST START_TEST (test_Reaction_getModifier) { SpeciesReference_t *msr1 = SpeciesReference_createModifier(2, 4); SpeciesReference_t *msr2 = SpeciesReference_createModifier(2, 4); SpeciesReference_setSpecies(msr1, "M1"); SpeciesReference_setSpecies(msr2, "M2"); Reaction_addModifier(R, msr1); Reaction_addModifier(R, msr2); SpeciesReference_free(msr1); SpeciesReference_free(msr2); fail_unless( Reaction_getNumReactants(R) == 0 ); fail_unless( Reaction_getNumProducts (R) == 0 ); fail_unless( Reaction_getNumModifiers(R) == 2 ); msr1 = Reaction_getModifier(R, 0); msr2 = Reaction_getModifier(R, 1); fail_unless(!strcmp(SpeciesReference_getSpecies(msr1), "M1")); fail_unless(!strcmp(SpeciesReference_getSpecies(msr2), "M2")); }
END_TEST START_TEST (test_Reaction_getModifierById) { SpeciesReference_t *msr1 = SpeciesReference_createModifier(2, 4); SpeciesReference_t *msr2 = SpeciesReference_createModifier(2, 4); SpeciesReference_setSpecies(msr1, "M1"); SpeciesReference_setSpecies(msr2, "M2"); Reaction_addModifier(R, msr1); Reaction_addModifier(R, msr2); fail_unless( Reaction_getNumReactants(R) == 0 ); fail_unless( Reaction_getNumProducts (R) == 0 ); fail_unless( Reaction_getNumModifiers(R) == 2 ); fail_unless( Reaction_getModifierBySpecies(R, "M1") != msr1 ); fail_unless( Reaction_getModifierBySpecies(R, "M2") != msr2 ); fail_unless( Reaction_getModifierBySpecies(R, "M3") == NULL ); SpeciesReference_free(msr1); SpeciesReference_free(msr2); }
END_TEST START_TEST (test_Reaction_addProductBySpecies) { Species_t *s = Species_create(2, 4); Species_setId(s, "s"); Reaction_addProductBySpecies(R, s, 2.0, "sr", 0); fail_unless( Reaction_getNumReactants(R) == 0 ); fail_unless( Reaction_getNumProducts (R) == 1 ); fail_unless( Reaction_getNumModifiers(R) == 0 ); SpeciesReference_t *sr = Reaction_getProduct(R, 0); fail_unless(!strcmp(SpeciesReference_getSpecies(sr), "s")); fail_unless(util_isEqual(SpeciesReference_getStoichiometry(sr), 2.0) == 1); fail_unless(!strcmp(SpeciesReference_getId(sr), "sr")); fail_unless(SpeciesReference_getConstant(sr) == 0); fail_unless(Reaction_addProductBySpecies(R, s, 1.0, "sr", 0) == LIBSBML_DUPLICATE_OBJECT_ID); fail_unless( Reaction_getNumProducts (R) == 1 ); Species_free(s); }
END_TEST START_TEST (test_Reaction_getProductById) { SpeciesReference_t *sr1 = SpeciesReference_create(2, 4); SpeciesReference_setSpecies(sr1, "P1"); SpeciesReference_t *sr2 = SpeciesReference_create(2, 4); SpeciesReference_setSpecies(sr2, "P1"); Reaction_addProduct(R, sr1); Reaction_addProduct(R, sr2); fail_unless( Reaction_getNumReactants(R) == 0 ); fail_unless( Reaction_getNumProducts (R) == 2 ); fail_unless( Reaction_getNumModifiers(R) == 0 ); fail_unless( Reaction_getProductBySpecies(R, "P1") != sr1 ); fail_unless( Reaction_getProductBySpecies(R, "P2") != sr2 ); fail_unless( Reaction_getProductBySpecies(R, "P3") == NULL ); SpeciesReference_free(sr1); SpeciesReference_free(sr2); }
END_TEST START_TEST (test_Reaction_removeModifier) { SpeciesReference_t *o1, *o2, *o3; o1 = Reaction_createModifier(R); o2 = Reaction_createModifier(R); o3 = Reaction_createModifier(R); SpeciesReference_setSpecies(o3, "test"); fail_unless( Reaction_removeModifier(R, 0) == o1 ); fail_unless( Reaction_getNumModifiers(R) == 2 ); fail_unless( Reaction_removeModifier(R, 0) == o2 ); fail_unless( Reaction_getNumModifiers(R) == 1 ); fail_unless( Reaction_removeModifierBySpecies(R,"test") == o3 ); fail_unless( Reaction_getNumModifiers(R) == 0 ); SpeciesReference_free(o1); SpeciesReference_free(o2); SpeciesReference_free(o3); }
END_TEST START_TEST (test_Reaction_addModifierBySpecies) { Species_t *s = Species_create(2, 4); Species_setId(s, "s"); Reaction_addModifierBySpecies(R, s, "sr"); fail_unless( Reaction_getNumReactants(R) == 0 ); fail_unless( Reaction_getNumProducts (R) == 0 ); fail_unless( Reaction_getNumModifiers(R) == 1 ); SpeciesReference_t *sr = Reaction_getModifier(R, 0); fail_unless(!strcmp(SpeciesReference_getSpecies(sr), "s")); fail_unless(!strcmp(SpeciesReference_getId(sr), "sr")); fail_unless(Reaction_addModifierBySpecies(R, s, "sr") == LIBSBML_DUPLICATE_OBJECT_ID); fail_unless( Reaction_getNumModifiers (R) == 1 ); Species_free(s); }
END_TEST START_TEST (test_Reaction_addModifier) { SpeciesReference_t * msr = SpeciesReference_createModifier(2, 4); SpeciesReference_setSpecies(msr, "s"); Reaction_addModifier(R, msr); fail_unless( Reaction_getNumReactants(R) == 0 ); fail_unless( Reaction_getNumProducts (R) == 0 ); fail_unless( Reaction_getNumModifiers(R) == 1 ); SpeciesReference_free(msr); }
END_TEST START_TEST (test_Reaction_addModifier3) { Reaction_t *m = Reaction_create(2, 2); SpeciesReference_t *p = NULL; int i = Reaction_addModifier(m, p); fail_unless( i == LIBSBML_OPERATION_FAILED); fail_unless( Reaction_getNumModifiers(m) == 0); Reaction_free(m); }
END_TEST START_TEST (test_Reaction_createModifier) { Reaction_t *m = Reaction_create(2, 2); SpeciesReference_t *p = Reaction_createModifier(m); fail_unless( Reaction_getNumModifiers(m) == 1); fail_unless( SBase_getLevel((SBase_t *) (p)) == 2 ); fail_unless( SBase_getVersion((SBase_t *) (p)) == 2 ); Reaction_free(m); }
END_TEST START_TEST (test_Reaction_addModifier2) { Reaction_t *m = Reaction_create(2, 2); SpeciesReference_t *p = SpeciesReference_createModifier(2, 1); SpeciesReference_setSpecies(p, "k"); int i = Reaction_addModifier(m, p); fail_unless( i == LIBSBML_VERSION_MISMATCH); fail_unless( Reaction_getNumModifiers(m) == 0); SpeciesReference_free(p); Reaction_free(m); }
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; }
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; }