END_TEST START_TEST (test_Compartment_setName) { const char *name = "My_Favorite_Factory"; Compartment_setName(C, name); fail_unless( !strcmp(Compartment_getName(C), name) ); fail_unless( Compartment_isSetName(C) ); if (Compartment_getName(C) == name) { fail("Compartment_setName(...) did not make a copy of string."); } /* Reflexive case (pathological) */ Compartment_setName(C, Compartment_getName(C)); fail_unless( !strcmp(Compartment_getName(C), name) ); Compartment_setName(C, NULL); fail_unless( !Compartment_isSetName(C) ); if (Compartment_getName(C) != NULL) { fail("Compartment_setName(C, NULL) did not clear string."); } }
END_TEST START_TEST (test_L3_Compartment_name) { const char *name = "My_Favorite_Factory"; fail_unless( !Compartment_isSetName(C) ); Compartment_setName(C, name); fail_unless( !strcmp(Compartment_getName(C), name) ); fail_unless( Compartment_isSetName(C) ); if (Compartment_getName(C) == name) { fail("Compartment_setName(...) did not make a copy of string."); } Compartment_unsetName(C); fail_unless( !Compartment_isSetName(C) ); if (Compartment_getName(C) != NULL) { fail("Compartment_unsetName(C) did not clear string."); } }
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_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"); } }
static int printXMGLegend(cvodeData_t *data, int nvalues) { int i, found; odeModel_t *om = data->model; Model_t *m = om->simple; Species_t *s; Parameter_t *p; Compartment_t *c; for ( i=0; i<nvalues; i++ ) { found = 0; if ( (s = Model_getSpeciesById(m, om->names[i])) != NULL ) { if ( Species_isSetName(s) ) { GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1, om->names[i], Species_getName(s)); found++; } } else if ( (c = Model_getCompartmentById(m, om->names[i])) ) { if ( Compartment_isSetName(c) ) { GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1, om->names[i], Compartment_getName(c)); found++; } } else if ( (p = Model_getParameterById(m, om->names[i])) ) { if ( Parameter_isSetName(p) ) { GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1, om->names[i], Parameter_getName(p)); found++; } } if ( found == 0 ) GracePrintf("g0.s%d legend \"%s\"\n", i+1, om->names[i]); } GracePrintf("legend 1.155, 0.85"); GracePrintf("legend font 8"); GracePrintf("legend char size 0.6"); return 0; }
void print_result_list(Model_t *m, mySpecies *mySp[], myParameter *myParam[], myCompartment *myComp[]){ FILE *fp = NULL; unsigned int i; int column = 2; if ((fp = my_fopen(fp, "./simulation_results/result_list.dat", "w")) == NULL) { return; } TRACE(("Result : Species List\n")); fprintf(fp, "Result : Species List\n"); for(i=0; i<Model_getNumSpecies(m); i++){ /* if(!(Species_getConstant(mySp[i]->origin) && Species_getBoundaryCondition(mySp[i]->origin))){ //XXX must remove this */ fprintf(fp, "column %d : ID=%s Name=%s\n", column, Species_getId(mySp[i]->origin), Species_getName(mySp[i]->origin)); column++; /* } */ } TRACE(("\n")); fprintf(fp, "\n"); fprintf(fp, "Result : Parameter List\n"); column = 2; for(i=0; i<Model_getNumParameters(m); i++){ /* if(!Parameter_getConstant(myParam[i]->origin)){ //XXX must remove this */ TRACE(("column %d : ID=%s Name=%s\n", column, Parameter_getId(myParam[i]->origin), Parameter_getName(myParam[i]->origin))); fprintf(fp, "column %d : ID=%s Name=%s\n", column, Parameter_getId(myParam[i]->origin), Parameter_getName(myParam[i]->origin)); column++; /* } */ } TRACE(("Result : Compartment List\n")); fprintf(fp, "Result : Compartment List\n"); column = 2; for(i=0; i<Model_getNumCompartments(m); i++){ /* if(!Compartment_getConstant(myComp[i]->origin)){ //XXX must remove this */ TRACE(("column %d : ID=%s Name=%s\n", column, Compartment_getId(myComp[i]->origin), Compartment_getName(myComp[i]->origin))); fprintf(fp, "column %d : ID=%s Name=%s\n", column, Compartment_getId(myComp[i]->origin), Compartment_getName(myComp[i]->origin)); column++; /* } */ } fclose(fp); }