END_TEST START_TEST (test_Species_getsetHasOnlySubstanceUnits) { // defaults fail_unless( Species_getHasOnlySubstanceUnits(S) == 0); fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1); Species_setHasOnlySubstanceUnits(S, 1); fail_unless( Species_getHasOnlySubstanceUnits(S) == 1); fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1); int ret = Species_unsetHasOnlySubstanceUnits(S); fail_unless(ret == LIBSBML_UNEXPECTED_ATTRIBUTE); fail_unless( Species_getHasOnlySubstanceUnits(S) == 0); fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1); Species_setHasOnlySubstanceUnits(S, 0); fail_unless( Species_getHasOnlySubstanceUnits(S) == 0); fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1); ret = Species_unsetHasOnlySubstanceUnits(S); fail_unless(ret == LIBSBML_UNEXPECTED_ATTRIBUTE); fail_unless( Species_getHasOnlySubstanceUnits(S) == 0); fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1); }
END_TEST START_TEST (test_L3_Species_hasOnlySubstanceUnits) { fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 0); Species_setHasOnlySubstanceUnits(S, 1); fail_unless(Species_getHasOnlySubstanceUnits(S) == 1); fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 1); int ret = Species_unsetHasOnlySubstanceUnits(S); fail_unless(ret == LIBSBML_OPERATION_SUCCESS); fail_unless(Species_getHasOnlySubstanceUnits(S) == 1); fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 0); Species_setHasOnlySubstanceUnits(S, 0); fail_unless(Species_getHasOnlySubstanceUnits(S) == 0); fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 1); ret = Species_unsetHasOnlySubstanceUnits(S); fail_unless(ret == LIBSBML_OPERATION_SUCCESS); fail_unless(Species_getHasOnlySubstanceUnits(S) == 0); fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 0); }
END_TEST START_TEST (test_L3_Species_initDefaults) { Species_t *s = Species_create(3,1); fail_unless( Species_getId (s) == NULL ); fail_unless( Species_getName (s) == NULL ); fail_unless( Species_getCompartment (s) == NULL ); fail_unless( util_isNaN(Species_getInitialAmount (s)) ); fail_unless( util_isNaN(Species_getInitialConcentration (s)) ); fail_unless( Species_getSubstanceUnits (s) == NULL ); fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 ); fail_unless( Species_getBoundaryCondition(s) == 0 ); fail_unless( Species_getConstant(s) == 0 ); fail_unless( Species_getConversionFactor (s) == NULL ); fail_unless( !Species_isSetId (s) ); fail_unless( !Species_isSetName (s) ); fail_unless( !Species_isSetCompartment (s) ); fail_unless( !Species_isSetInitialAmount (s) ); fail_unless( !Species_isSetInitialConcentration (s) ); fail_unless( !Species_isSetSubstanceUnits (s) ); fail_unless( !Species_isSetHasOnlySubstanceUnits(s) ); fail_unless( !Species_isSetBoundaryCondition(s) ); fail_unless( !Species_isSetConstant(s) ); fail_unless( !Species_isSetConversionFactor (s) ); Species_initDefaults(s); fail_unless( Species_getId (s) == NULL ); fail_unless( Species_getName (s) == NULL ); fail_unless( Species_getCompartment (s) == NULL ); fail_unless( util_isNaN(Species_getInitialAmount (s)) ); fail_unless( util_isNaN(Species_getInitialConcentration (s)) ); fail_unless( !strcmp(Species_getSubstanceUnits (s),"mole" )); fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 ); fail_unless( Species_getBoundaryCondition(s) == 0 ); fail_unless( Species_getConstant(s) == 0 ); fail_unless( Species_getConversionFactor (s) == NULL ); fail_unless( !Species_isSetId (s) ); fail_unless( !Species_isSetName (s) ); fail_unless( !Species_isSetCompartment (s) ); fail_unless( !Species_isSetInitialAmount (s) ); fail_unless( !Species_isSetInitialConcentration (s) ); fail_unless( Species_isSetSubstanceUnits (s) ); fail_unless( Species_isSetHasOnlySubstanceUnits(s) ); fail_unless( Species_isSetBoundaryCondition(s) ); fail_unless( Species_isSetConstant(s) ); fail_unless( !Species_isSetConversionFactor (s) ); Species_free(s); }
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_L3_Species_hasOnlySubstanceUnits) { fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 0); Species_setHasOnlySubstanceUnits(S, 1); fail_unless(Species_getHasOnlySubstanceUnits(S) == 1); fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 1); Species_setHasOnlySubstanceUnits(S, 0); fail_unless(Species_getHasOnlySubstanceUnits(S) == 0); fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 1); }
END_TEST START_TEST (test_Species_setHasOnlySubstanceUnits1) { int i = Species_setHasOnlySubstanceUnits(C, 0); fail_unless( Species_getHasOnlySubstanceUnits(C) == 0 ); fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE ); }
END_TEST START_TEST (test_Species_setHasOnlySubstanceUnits2) { Species_t *c = Species_create(2, 2); int i = Species_setHasOnlySubstanceUnits(c, 0); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( Species_getHasOnlySubstanceUnits(c) == 0 ); i = Species_setHasOnlySubstanceUnits(c, 1); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( Species_getHasOnlySubstanceUnits(c) == 1 ); Species_free(c); }
END_TEST START_TEST (test_L3_Species_createWithNS ) { XMLNamespaces_t *xmlns = XMLNamespaces_create(); XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml"); SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1); SBMLNamespaces_addNamespaces(sbmlns,xmlns); Species_t *s = Species_createWithNS (sbmlns); fail_unless( SBase_getTypeCode ((SBase_t *) s) == SBML_SPECIES ); fail_unless( SBase_getMetaId ((SBase_t *) s) == NULL ); fail_unless( SBase_getNotes ((SBase_t *) s) == NULL ); fail_unless( SBase_getAnnotation((SBase_t *) s) == NULL ); fail_unless( SBase_getLevel ((SBase_t *) s) == 3 ); fail_unless( SBase_getVersion ((SBase_t *) s) == 1 ); fail_unless( Species_getNamespaces (s) != NULL ); fail_unless( XMLNamespaces_getLength(Species_getNamespaces(s)) == 2 ); fail_unless( Species_getId (s) == NULL ); fail_unless( Species_getName (s) == NULL ); fail_unless( Species_getCompartment (s) == NULL ); fail_unless( util_isNaN(Species_getInitialAmount (s)) ); fail_unless( util_isNaN(Species_getInitialConcentration (s)) ); fail_unless( Species_getSubstanceUnits (s) == NULL ); fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 ); fail_unless( Species_getBoundaryCondition(s) == 0 ); fail_unless( Species_getConstant(s) == 0 ); fail_unless( Species_getConversionFactor (s) == NULL ); fail_unless( !Species_isSetId (s) ); fail_unless( !Species_isSetName (s) ); fail_unless( !Species_isSetCompartment (s) ); fail_unless( !Species_isSetInitialAmount (s) ); fail_unless( !Species_isSetInitialConcentration (s) ); fail_unless( !Species_isSetSubstanceUnits (s) ); fail_unless( !Species_isSetHasOnlySubstanceUnits(s) ); fail_unless( !Species_isSetBoundaryCondition(s) ); fail_unless( !Species_isSetConstant(s) ); fail_unless( !Species_isSetConversionFactor (s) ); Species_free(s); XMLNamespaces_free(xmlns); SBMLNamespaces_free(sbmlns); }
END_TEST START_TEST (test_SBMLConvertStrict_convertToL1) { SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4); /* create model with metaid */ Model_t * m = SBMLDocument_createModel(d); SBase_setMetaId((SBase_t *) (m), "_m"); /* create a compartment with sbo*/ Compartment_t * c = Model_createCompartment(m); Compartment_setId(c, "c"); SBase_setSBOTerm((SBase_t *) (c), 240); /* create a species with hasOnlySubstanceUnits = true*/ Species_t *s = Model_createSpecies(m); Species_setId(s, "s"); Species_setCompartment(s, "c"); Species_setHasOnlySubstanceUnits(s, 1); fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 1, 2) == 1 ); fail_unless( SBMLDocument_getLevel (d) == 1, NULL ); fail_unless( SBMLDocument_getVersion(d) == 2, NULL ); ///* check that attributes that are no longer valid have been removed */ Model_t * m1 = SBMLDocument_getModel(d); fail_unless (SBase_getMetaId((SBase_t *) (m1)) == NULL); Compartment_t *c1 = Model_getCompartment(m1, 0); fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL ); Species_t *s1 = Model_getSpecies(m1, 0); fail_unless (Species_getHasOnlySubstanceUnits(s1) == 0); SBMLDocument_free(d); }
/* setValues: the user can enter a species name and change its initial condition (amount or concentration) */ static void setValues(Model_t *m) { char *species; char *newIA; char *newIC; Species_t *s; printf("Please enter the id of the species to change: "); species = get_line(stdin); species = util_trim(species); if ( (s = Model_getSpeciesById(m,species) ) ) { printf("\n"); printf("Id: %s\n", Species_getId(s)); if ( Species_isSetName(s) ) { printf("Name: %s\n", Species_getName(s)); } if ( Species_isSetInitialAmount(s) ) { printf("Initial Amount: %g", Species_getInitialAmount(s)); } else if (Species_isSetInitialConcentration(s) ) { printf("Initial Concentration: %g", Species_getInitialConcentration(s)); } if ( Species_getHasOnlySubstanceUnits(s) ) { if ( Species_isSetSubstanceUnits(s) ) { printf("%s ", Species_getSubstanceUnits(s)); } } else { if ( Species_isSetSubstanceUnits(s) ) { printf("%s ", Species_getSubstanceUnits(s)); } if ( Species_isSetSpatialSizeUnits(s) ) { printf("%s%s", "/", Species_getSpatialSizeUnits(s)); } } if ( Species_getHasOnlySubstanceUnits(s) ) { printf(" (has only substance units)"); } printf("\n"); if ( Species_isSetCharge(s) ) { printf("Charge: %-10d", Species_getCharge(s)); } printf("\n"); printf("%s ", Species_getBoundaryCondition(s) ? "Species is a Boundary\n" : "\n"); printf("%s ", Species_getConstant(s) ? "Species is set constant" : "\n"); printf("\n"); if ( Species_isSetInitialAmount(s) ) { printf("Please enter new initial Amount: "); newIA = get_line(stdin); newIA = util_trim(newIA); Species_setInitialAmount(s, (float) atof(newIA)); } else if ( Species_isSetInitialConcentration(s) ) { printf("Please enter new initial Concentration: "); newIC = get_line(stdin); newIC = util_trim(newIC); Species_setInitialConcentration(s, (float) atof(newIC)); } } else { printf("%s not found.\n", species); } }