END_TEST START_TEST (test_FormulaFormatter_multiOr) { StringBuffer_t *sb = StringBuffer_create(42); char *s = StringBuffer_getBuffer(sb); ASTNode_t *n = ASTNode_create(); ASTNode_t *c = ASTNode_create(); ASTNode_setType(n, AST_LOGICAL_OR); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "or()"), NULL ); ASTNode_setName(c, "x"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "or(x)"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "y"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "or(x, y)"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "z"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "or(x, y, z)"), NULL ); safe_free(s); ASTNode_free(n); }
END_TEST START_TEST (test_FormulaFormatter_multiPlusTimes) { StringBuffer_t *sb = StringBuffer_create(42); char *s = StringBuffer_getBuffer(sb); ASTNode_t *n = ASTNode_create(); ASTNode_t *c = ASTNode_create(); ASTNode_setType(n, AST_PLUS); ASTNode_setName(c, "x"); ASTNode_addChild(n, c); c = ASTNode_create(); ASTNode_setName(c, "y"); ASTNode_addChild(n, c); c = ASTNode_create(); ASTNode_setName(c, "z"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "x + y + z"), NULL ); ASTNode_setType(n, AST_TIMES); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "x * y * z"), NULL ); safe_free(s); ASTNode_free(n); }
END_TEST START_TEST (test_FormulaFormatter_multiDivide) { StringBuffer_t *sb = StringBuffer_create(42); char *s = StringBuffer_getBuffer(sb); ASTNode_t *n = ASTNode_create(); ASTNode_t *c = ASTNode_create(); ASTNode_setType(n, AST_DIVIDE); s = SBML_formulaToString(n); fail_unless( !strcmp(s, " / "), NULL ); ASTNode_setName(c, "x"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, " / (x)"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "y"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "x / y"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "z"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "x / y / z"), NULL ); safe_free(s); ASTNode_free(n); }
END_TEST START_TEST (test_Rule_setMath1) { ASTNode_t *math = ASTNode_createWithType(AST_TIMES); ASTNode_t *a = ASTNode_create(); ASTNode_t *b = ASTNode_create(); ASTNode_setName(a, "a"); ASTNode_setName(b, "b"); ASTNode_addChild(math, a); ASTNode_addChild(math, b); char *formula; const ASTNode_t *math1; int i = Rule_setMath(R, math); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( Rule_isSetMath(R) ); math1 = Rule_getMath(R); fail_unless( math1 != NULL ); formula = SBML_formulaToString(math1); fail_unless( formula != NULL ); fail_unless( !strcmp(formula, "a * b") ); ASTNode_free(math); }
END_TEST START_TEST (test_L3FormulaFormatter_multiGT) { StringBuffer_t *sb = StringBuffer_create(42); char *s = StringBuffer_getBuffer(sb); ASTNode_t *n = ASTNode_create(); ASTNode_t *c = ASTNode_create(); ASTNode_setType(n, AST_RELATIONAL_GT); s = SBML_formulaToL3String(n); fail_unless( !strcmp(s, "gt()"), NULL ); ASTNode_setName(c, "x"); ASTNode_addChild(n, c); s = SBML_formulaToL3String(n); fail_unless( !strcmp(s, "gt(x)"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "y"); ASTNode_addChild(n, c); s = SBML_formulaToL3String(n); fail_unless( !strcmp(s, "x > y"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "z"); ASTNode_addChild(n, c); s = SBML_formulaToL3String(n); fail_unless( !strcmp(s, "gt(x, y, z)"), NULL ); safe_free(s); ASTNode_free(n); }
END_TEST START_TEST (test_L3FormulaFormatter_multiAnd) { StringBuffer_t *sb = StringBuffer_create(42); char *s = StringBuffer_getBuffer(sb); ASTNode_t *n = ASTNode_create(); ASTNode_t *c = ASTNode_create(); ASTNode_setType(n, AST_LOGICAL_AND); s = SBML_formulaToL3String(n); fail_unless( !strcmp(s, "and()"), NULL ); ASTNode_setName(c, "x"); ASTNode_addChild(n, c); s = SBML_formulaToL3String(n); fail_unless( !strcmp(s, "and(x)"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "y"); ASTNode_addChild(n, c); s = SBML_formulaToL3String(n); fail_unless( !strcmp(s, "x && y"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "z"); ASTNode_addChild(n, c); s = SBML_formulaToL3String(n); fail_unless( !strcmp(s, "x && y && z"), NULL ); safe_free(s); ASTNode_free(n); }
END_TEST START_TEST (test_SpeciesReference_setStoichiometryMath5) { SpeciesReference_t *sr1 = SpeciesReference_create(1, 2); StoichiometryMath_t * sm = StoichiometryMath_create(2, 4); ASTNode_t *math = ASTNode_createWithType(AST_TIMES); ASTNode_t *a = ASTNode_create(); ASTNode_t *b = ASTNode_create(); ASTNode_setName(a, "a"); ASTNode_setName(b, "b"); ASTNode_addChild(math, a); ASTNode_addChild(math, b); StoichiometryMath_setMath(sm, math); int i = SpeciesReference_setStoichiometryMath(sr1, sm); fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE); fail_unless( !SpeciesReference_isSetStoichiometryMath(sr1) ); StoichiometryMath_free(sm); SpeciesReference_free(sr1); }
END_TEST START_TEST (test_SpeciesReference_setStoichiometryMath1) { StoichiometryMath_t * sm = StoichiometryMath_create(2, 4); ASTNode_t *math = ASTNode_createWithType(AST_TIMES); ASTNode_t *a = ASTNode_create(); ASTNode_t *b = ASTNode_create(); ASTNode_setName(a, "a"); ASTNode_setName(b, "b"); ASTNode_addChild(math, a); ASTNode_addChild(math, b); StoichiometryMath_setMath(sm, math); int i = SpeciesReference_setStoichiometryMath(sr, sm); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( SpeciesReference_isSetStoichiometryMath(sr) ); fail_unless( SpeciesReference_getStoichiometry(sr) == 1 ); i = SpeciesReference_unsetStoichiometryMath(sr); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( !SpeciesReference_isSetStoichiometryMath(sr) ); StoichiometryMath_free(sm); }
END_TEST START_TEST (test_FormulaFormatter_multiAnd) { char *s; ASTNode_t *n = ASTNode_create(); ASTNode_t *c = ASTNode_create(); ASTNode_setType(n, AST_LOGICAL_AND); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "and()"), NULL ); safe_free(s); ASTNode_setName(c, "x"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "and(x)"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "y"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "and(x, y)"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "z"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "and(x, y, z)"), NULL ); safe_free(s); ASTNode_free(n); }
END_TEST START_TEST (test_FormulaFormatter_multiPlus) { char *s; ASTNode_t *n = ASTNode_create(); ASTNode_t *c = ASTNode_create(); ASTNode_setType(n, AST_PLUS); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "0"), NULL ); safe_free(s); ASTNode_setName(c, "x"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "x"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "y"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "x + y"), NULL ); safe_free(s); c = ASTNode_create(); ASTNode_setName(c, "z"); ASTNode_addChild(n, c); s = SBML_formulaToString(n); fail_unless( !strcmp(s, "x + y + z"), NULL ); safe_free(s); ASTNode_free(n); }
void post_ev_alter_tree_structure(Model_t *m, ASTNode_t **node_p, ASTNode_t *parent, int child_order){ ASTNode_t *divide_node, *times_node; ASTNode_t *compartment_node; ASTNode_t *node, *next_node; unsigned int i; Species_t *sp; node = *node_p; for(i=0; i<ASTNode_getNumChildren(node); i++){ next_node = ASTNode_getChild(node, i); post_ev_alter_tree_structure(m, &next_node, *node_p, i); } if(ASTNode_getType(node) == AST_NAME){ for(i=0; i<Model_getNumSpecies(m); i++){ sp = (Species_t*)ListOf_get(Model_getListOfSpecies(m), i); if(strcmp(Species_getId(sp), ASTNode_getName(node)) == 0){ if(!Species_getHasOnlySubstanceUnits(sp) && Compartment_getSpatialDimensions(Model_getCompartmentById(m, Species_getCompartment(sp))) != 0){/* use val/comp in calculation */ divide_node = ASTNode_createWithType(AST_DIVIDE); compartment_node = ASTNode_createWithType(AST_NAME); ASTNode_setName(compartment_node, Compartment_getId(Model_getCompartmentById(m, Species_getCompartment(sp)))); ASTNode_addChild(divide_node, node); ASTNode_addChild(divide_node, compartment_node); if(parent != NULL){ ASTNode_replaceChild(parent, child_order, divide_node); }else{ *node_p = divide_node; } node = *node_p; break; }else if(Species_getHasOnlySubstanceUnits(sp) && Species_isSetInitialConcentration(sp) && Compartment_getSpatialDimensions(Model_getCompartmentById(m, Species_getCompartment(sp))) != 0){/* use val*comp in calculation */ times_node = ASTNode_createWithType(AST_TIMES); compartment_node = ASTNode_createWithType(AST_NAME); ASTNode_setName(compartment_node, Compartment_getId(Model_getCompartmentById(m, Species_getCompartment(sp)))); ASTNode_addChild(times_node, node); ASTNode_addChild(times_node, compartment_node); if(parent != NULL){ ASTNode_replaceChild(parent, child_order, times_node); }else{ *node_p = times_node; } node = *node_p; break; } } } } return; }
END_TEST START_TEST (test_Rule_setMath2) { ASTNode_t *math = ASTNode_createWithType(AST_DIVIDE); ASTNode_t *a = ASTNode_create(); ASTNode_setName(a, "a"); ASTNode_addChild(math, a); int i = Rule_setMath(R, math); fail_unless( i == LIBSBML_INVALID_OBJECT); fail_unless( !Rule_isSetMath(R) ); ASTNode_free(math); }
END_TEST START_TEST (test_KineticLaw_setMath2) { ASTNode_t *math = ASTNode_createWithType(AST_TIMES); ASTNode_t *a = ASTNode_create(); ASTNode_setName(a, "a"); ASTNode_addChild(math, a); int i = KineticLaw_setMath(kl, math); fail_unless( i == LIBSBML_INVALID_OBJECT); fail_unless( !KineticLaw_isSetMath(kl) ); ASTNode_free(math); }
END_TEST START_TEST (test_L3FormulaFormatter_collapseMinus) { StringBuffer_t *sb = StringBuffer_create(42); char *s = StringBuffer_getBuffer(sb); ASTNode_t *n = ASTNode_create(); ASTNode_t *c = ASTNode_create(); ASTNode_t *c2 = ASTNode_create(); ASTNode_t *c3 = ASTNode_create(); ASTNode_t *c4 = ASTNode_create(); L3ParserSettings_t* l3ps = L3ParserSettings_create(); ASTNode_setType(n, AST_MINUS); ASTNode_setType(c, AST_MINUS); ASTNode_addChild(n, c); ASTNode_setType(c2, AST_MINUS); ASTNode_addChild(c, c2); ASTNode_setType(c3, AST_MINUS); ASTNode_addChild(c2, c3); ASTNode_setName(c4, "x"); ASTNode_addChild(c3, c4); //default (false) s = SBML_formulaToL3StringWithSettings(n, l3ps); fail_unless( !strcmp(s, "----x"), NULL ); safe_free(s); //explicit false L3ParserSettings_setParseCollapseMinus(l3ps, 0); s = SBML_formulaToL3StringWithSettings(n, l3ps); fail_unless( !strcmp(s, "----x"), NULL ); safe_free(s); //explicit true L3ParserSettings_setParseCollapseMinus(l3ps, 1); s = SBML_formulaToL3StringWithSettings(n, l3ps); fail_unless( !strcmp(s, "x"), NULL ); safe_free(s); ASTNode_free(n); L3ParserSettings_free(l3ps); }
END_TEST START_TEST (test_SpeciesReference_setStoichiometryMath2) { StoichiometryMath_t * sm = StoichiometryMath_create(2, 4); ASTNode_t *math = ASTNode_createWithType(AST_TIMES); ASTNode_t *a = ASTNode_create(); ASTNode_setName(a, "a"); ASTNode_addChild(math, a); StoichiometryMath_setMath(sm, math); int i = SpeciesReference_setStoichiometryMath(sr, sm); /* once the StoichiometryMath_setMath function does not set * an invalid ASTNode this changes to i == LIBSBML_OPERATION_SUCCESS fail_unless( i == LIBSBML_INVALID_OBJECT); */ fail_unless ( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( SpeciesReference_isSetStoichiometryMath(sr) ); StoichiometryMath_free(sm); }
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; }