END_TEST START_TEST (test_Compartment_initDefaults) { Compartment_t *c = Compartment_create(2, 4); Compartment_setId(c, "A"); Compartment_initDefaults(c); fail_unless( !strcmp(Compartment_getId (c), "A")); fail_unless( Compartment_getName (c) == NULL ); fail_unless( Compartment_getUnits (c) == NULL ); fail_unless( Compartment_getOutside(c) == NULL ); fail_unless( Compartment_getSpatialDimensions(c) == 3 ); fail_unless( Compartment_getVolume (c) == 1.0 ); fail_unless( Compartment_getConstant (c) == 1 ); fail_unless( Compartment_isSetId (c) ); fail_unless( !Compartment_isSetName (c) ); fail_unless( !Compartment_isSetSize (c) ); fail_unless( !Compartment_isSetVolume (c) ); fail_unless( !Compartment_isSetUnits (c) ); fail_unless( !Compartment_isSetOutside(c) ); fail_unless( Compartment_isSetSpatialDimensions(c) ); fail_unless( Compartment_isSetConstant(c) ); Compartment_free(c); }
END_TEST START_TEST (test_Compartment_getSpatialDimensions) { fail_unless( Compartment_isSetSpatialDimensions(C) ); fail_unless( Compartment_getSpatialDimensions(C) == 3); Compartment_setSpatialDimensions(C, 1); fail_unless( Compartment_getSpatialDimensions(C) == 1); fail_unless( Compartment_isSetSpatialDimensions(C) ); fail_unless( Compartment_unsetSpatialDimensions(C) == LIBSBML_UNEXPECTED_ATTRIBUTE); fail_unless( Compartment_getSpatialDimensions(C) == 3); fail_unless( Compartment_isSetSpatialDimensions(C) ); }
END_TEST START_TEST (test_Compartment_createWithNS ) { XMLNamespaces_t *xmlns = XMLNamespaces_create(); XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml"); SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(2,1); SBMLNamespaces_addNamespaces(sbmlns,xmlns); Compartment_t *c = Compartment_createWithNS (sbmlns); fail_unless( SBase_getTypeCode ((SBase_t *) c) == SBML_COMPARTMENT ); fail_unless( SBase_getMetaId ((SBase_t *) c) == NULL ); fail_unless( SBase_getNotes ((SBase_t *) c) == NULL ); fail_unless( SBase_getAnnotation((SBase_t *) c) == NULL ); fail_unless( SBase_getLevel ((SBase_t *) c) == 2 ); fail_unless( SBase_getVersion ((SBase_t *) c) == 1 ); fail_unless( Compartment_getNamespaces (c) != NULL ); fail_unless( XMLNamespaces_getLength(Compartment_getNamespaces(c)) == 2 ); fail_unless( Compartment_getName(c) == NULL ); fail_unless( Compartment_getSpatialDimensions(c) == 3 ); fail_unless( Compartment_getConstant(c) == 1 ); Compartment_free(c); XMLNamespaces_free(xmlns); SBMLNamespaces_free(sbmlns); }
END_TEST START_TEST (test_Compartment_createWith) { Compartment_t *c = Compartment_create(2, 4); Compartment_setId(c, "A"); fail_unless( SBase_getTypeCode ((SBase_t *) c) == SBML_COMPARTMENT ); fail_unless( SBase_getMetaId ((SBase_t *) c) == NULL ); fail_unless( SBase_getNotes ((SBase_t *) c) == NULL ); fail_unless( SBase_getAnnotation((SBase_t *) c) == NULL ); fail_unless( Compartment_getName(c) == NULL ); fail_unless( Compartment_getSpatialDimensions(c) == 3 ); fail_unless( !strcmp( Compartment_getId (c), "A" ) ); fail_unless( Compartment_getConstant(c) == 1 ); fail_unless( Compartment_isSetId (c) ); fail_unless( !Compartment_isSetName (c) ); Compartment_free(c); }
void printSpecies(Model_t *m, FILE *f) { int i, j; Species_t *s; Compartment_t *c; fprintf(f, "\n"); fprintf(f, "# Initial Conditions for Species and Compartments:\n"); for ( i=0; i<Model_getNumCompartments(m); i++ ) { if ( i== 0 ) fprintf(f, "# Compartments:\n"); c = Model_getCompartment(m,i); if(Compartment_isSetId(c)) fprintf(f, "%s ", Compartment_getId(c)); if(Compartment_isSetName(c)) fprintf(f, "(%s) ", Compartment_getName(c)); if ( Compartment_isSetVolume(c) ) fprintf(f, "= %g; ", Compartment_getSize(c)); fprintf(f, "%s", Compartment_getConstant(c) ? "" : "variable; "); if(Compartment_isSetOutside(c)) fprintf(f, "outside %s; ", Compartment_getOutside(c)); /* fprintf(f, "\n"); */ fprintf(f, "dimensions %d; ", Compartment_getSpatialDimensions(c)); if(Compartment_isSetUnits(c)) fprintf(f, "[%s]; ", Compartment_getUnits(c)); fprintf(f, "\n"); fprintf(f, "# Species concentrations in `compartment' %s\n", Compartment_getId(c)); for(j=0;j<Model_getNumSpecies(m);j++){ s = Model_getSpecies(m,j); if(strcmp(Species_getCompartment(s), Compartment_getId(c))==0){ fprintf(f, "%s ", Species_getId(s)); if(Species_isSetName(s)) fprintf(f, "(%s) ", Species_getName(s)); if ( Species_isSetInitialAmount(s) ) fprintf(f, "= %g/%g; ", Species_getInitialAmount(s), Compartment_getSize(c)); else if ( Species_isSetInitialConcentration(s) ) fprintf(f, "= %g; ", Species_getInitialConcentration(s)); else fprintf(f, "# no initial value;"); fprintf(f, "%s", Species_getBoundaryCondition(s) ? "boundary;" : ""); fprintf(f, "%s", Species_getConstant(s) ? "constant;" : ""); if(Species_isSetCharge(s)) fprintf(f, "charge = %d; ", Species_getCharge(s)); fprintf(f, "\n"); } } fprintf(f, "\n"); } }
END_TEST START_TEST (test_Compartment_getSpatialDimensions) { Compartment_setSpatialDimensions(C, 1); fail_unless( Compartment_getSpatialDimensions(C) == 1); }
END_TEST START_TEST (test_Compartment_setSpatialDimensions1) { int i = Compartment_setSpatialDimensions(C, 2); fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE ); fail_unless( Compartment_getSpatialDimensions(C) == 3 ); }
END_TEST START_TEST (test_Compartment_setSpatialDimensions5) { Compartment_t *c = Compartment_create(2, 2); int i = Compartment_setSpatialDimensionsAsDouble(c, 2.2); fail_unless( i == LIBSBML_INVALID_ATTRIBUTE_VALUE ); fail_unless( Compartment_getSpatialDimensions(c) == 3 ); Compartment_free(c); }
END_TEST START_TEST (test_Compartment_setSpatialDimensions4) { Compartment_t *c = Compartment_create(2, 2); int i = Compartment_setSpatialDimensionsAsDouble(c, 2.0); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( Compartment_getSpatialDimensions(c) == 2 ); Compartment_free(c); }
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; }