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_setVolume1)
{
int i = Compartment_setVolume(C, 2.0);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Compartment_getVolume(C) == 2.0 );
fail_unless( Compartment_isSetVolume(C));
i = Compartment_unsetVolume(C);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Compartment_getVolume(C) == 1.0 );
fail_unless( Compartment_isSetVolume(C));
}
END_TEST
START_TEST (test_L3_Compartment_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);
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) == 3 );
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_getId (c) == NULL );
fail_unless( Compartment_getName (c) == NULL );
fail_unless( Compartment_getUnits (c) == NULL );
fail_unless( Compartment_getOutside(c) == NULL );
fail_unless( util_isNaN(Compartment_getSpatialDimensionsAsDouble(c)) );
fail_unless( util_isNaN(Compartment_getVolume(c)));
fail_unless( Compartment_getConstant(c) == 1 );
fail_unless( !Compartment_isSetId (c) );
fail_unless( !Compartment_isSetSpatialDimensions (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_isSetConstant(c) );
Compartment_free(c);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_Compartment_unsetVolume)
{
Compartment_setVolume(C, 1.0);
fail_unless( Compartment_getVolume(C) == 1.0 );
/* FIX_ME
fail_unless( Compartment_isSetVolume(C) );
*/
Compartment_unsetVolume(C);
fail_unless( !Compartment_isSetVolume(C) );
}
END_TEST
START_TEST (test_Compartment_setVolume2)
{
Compartment_t *c =
Compartment_create(2, 2);
int i = Compartment_setVolume(c, 4);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Compartment_getVolume(c) == 4.0 );
fail_unless( Compartment_isSetVolume(c));
i = Compartment_unsetVolume(c);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Compartment_isSetVolume(c));
Compartment_free(c);
}
int main(int argc, char** argv)
{
myspecies_t* species; //pinakas ximikon stoixeion
reaction_t *reaction; //20 ximikes antidraseis
int i,j,k,num_species, num_reactions;
double V;
FILE *pf1, *pf2, *pf3, *pf4, *pf5, *pf6, *fsize;
SBMLDocument_t *d;
Model_t *m;
ListOf_t *lo;
Species_t *sp;
Reaction_t *re;
Parameter_t *p;
KineticLaw_t *kin;
SpeciesReference_t *sr;
Compartment_t *c;
//an den exei 2 argument
if(argc != 2)
{
printf("Ektelesi: %s <SBML xml>\n", argv[0]);
exit(-1);
}
//arxeia results
if((pf1 = fopen("RT_reactant.txt", "w")) == NULL)
{
printf("Error create file %s\n","RT_reactant.txt");
exit(-1);
}
if((pf2 = fopen("RT_product.txt", "w")) == NULL)
{
printf("Error create file %s\n","RT_product.txt");
fclose(pf1);
exit(-1);
}
if((pf3 = fopen("VT_reactant.txt", "w")) == NULL)
{
printf("Error create file %s\n","VT_reactant.txt");
fclose(pf1);
fclose(pf2);
exit(-1);
}
if((pf4 = fopen("VT_product.txt", "w")) == NULL)
{
printf("Error create file %s\n","VT_product.txt");
fclose(pf1);
fclose(pf2);
fclose(pf3);
exit(-1);
}
if((pf5 = fopen("ST.txt", "w")) == NULL)
{
printf("Error create file %s\n","ST.txt");
fclose(pf1);
fclose(pf2);
fclose(pf3);
fclose(pf4);
exit(-1);
}
if((pf6 = fopen("k_parameter.txt", "w")) == NULL)
{
printf("Error create file %s\n","k_parameter.txt");
fclose(pf1);
fclose(pf2);
fclose(pf3);
fclose(pf4);
fclose(pf5);
exit(-1);
}
fsize = fopen("fsize.txt", "w");
//anoigo to SBML arxeio
d = readSBML(argv[1]);
//d=readSBML("C:/home/orsalia/BIOMD0000000001");
m = SBMLDocument_getModel(d);
num_species = Model_getNumSpecies(m);
num_reactions = Model_getNumReactions(m);
fprintf(fsize,"%d\n",num_species);
fprintf(fsize,"%d\n",num_reactions);
//Pairnoume ton ogko
c = Model_getCompartment(m,0);
V = Compartment_getVolume(c);
//Desmeysi pinakon domon gia stoixeia kai reaction
species = (myspecies_t*) malloc(num_species*sizeof(myspecies_t));
reaction = (reaction_t*) malloc(num_reactions*sizeof(reaction_t));
//gemizo ton pinaka me tis arxikes sigkentroseis ton stoixeion
for(i=0;i<num_species;i++)
{
sp = Model_getSpecies(m,i);
species[i].conc = Species_getInitialConcentration(sp)?Species_getInitialConcentration(sp):Species_getInitialAmount(sp);
species[i].name = malloc(50*sizeof(char));
strcpy(species[i].name,Species_getId(sp));
strcpy(species[i].name2,Species_getName(sp));
}
///gemizo ton pinaka domon ton reaction
for(i=0;i<num_reactions;i++)
{
re = Model_getReaction(m,i);
kin = Reaction_getKineticLaw(re);
p = KineticLaw_getParameter(kin,0);
reaction[i].react_num = Reaction_getNumReactants(re);
reaction[i].product_num = Reaction_getNumProducts(re);
reaction[i].react = (x_vector_t*) malloc(reaction[i].react_num*sizeof(x_vector_t));
reaction[i].product = (x_vector_t*) malloc(reaction[i].product_num*sizeof(x_vector_t));
for(j=0;j<reaction[i].react_num;j++)
{
sr = Reaction_getReactant(re,j);
for(k=0;k<num_species;k++)
{
//an vrei to stoixeio ston megalo pinaka krata ti thesi tou
if (strcmp(SpeciesReference_getSpecies(sr),species[k].name) == 0)
{
reaction[i].react[j].x = k; //ithesi ston pinaka species
reaction[i].react[j].v = (-1) * SpeciesReference_getStoichiometry(sr);
break;
}
}
}
for(j=0;j<reaction[i].product_num;j++)
{
sr = Reaction_getProduct(re,j);
for(k=0;k<num_species;k++)
{
//an vrei to stoixeio ston megalo pinaka krata ti thesi tou
if (strcmp(SpeciesReference_getSpecies(sr),species[k].name) == 0)
{
reaction[i].product[j].x = k; //ithesi ston pinaka species
reaction[i].product[j].v = SpeciesReference_getStoichiometry(sr);
break;
}
}
}
reaction[i].k = Parameter_getValue(p);
//vlepo tin eidos antidraseis einai kai vazo to c tis kathe antidrasis
if(reaction[i].react_num == 3)
{
reaction[i].type = 7;
reaction[i].c = Parameter_getValue(p)/(V*V); //mallon
}
else if(reaction[i].react_num == 2)
{
sr = Reaction_getReactant(re,0);
if (SpeciesReference_getStoichiometry(sr) == 2 )
{
reaction[i].type = 5;
reaction[i].c = 2*Parameter_getValue(p)/(V*V); //oute kan
}
else
{
sr = Reaction_getReactant(re,1);
if (SpeciesReference_getStoichiometry(sr) == 2 )
{
reaction[i].type = 6;
reaction[i].c = 2*Parameter_getValue(p)/(V*V); //oute kan
}
else
{
reaction[i].type = 2;
reaction[i].c = Parameter_getValue(p)/V;
}
}
}
else //if(reaction[i].react_num == 1)
{
sr = Reaction_getReactant(re,0);
if (SpeciesReference_getStoichiometry(sr) == 2 ) //an einai bimolecular me to idio stoixeio
{
reaction[i].type = 3;
reaction[i].c = 2*Parameter_getValue(p)/V;
}
else if(SpeciesReference_getStoichiometry(sr) == 3 )
{
reaction[i].type = 4;
reaction[i].c = 3*Parameter_getValue(p)/(V*V); //mallon
}
else
{
reaction[i].type = 1;
reaction[i].c = Parameter_getValue(p);
}
}
}
for(i=0;i<num_species;i++)
{
//fprintf(pf5,"%d\t%s\n",(int)species[i].conc,species[i].name2);
fprintf(pf5,"%d\t\n",(int)species[i].conc);
}
for(i=0;i<num_reactions;i++)
{
for(k=0;k<reaction[i].react_num;k++)
{
fprintf(pf1,"%d\t",reaction[i].react[k].x+1);
fprintf(pf3,"%d\t",reaction[i].react[k].v);
}
for(k=0;k<reaction[i].product_num;k++)
{
fprintf(pf2,"%d\t",reaction[i].product[k].x+1);
fprintf(pf4,"%d\t",reaction[i].product[k].v);
}
fprintf(pf1,"\n");
fprintf(pf3,"\n");
fprintf(pf2,"\n");
fprintf(pf4,"\n");
fprintf(pf6,"%f\n",reaction[i].k);
}
fclose(pf1);
fclose(pf2);
fclose(pf3);
fclose(pf4);
fclose(pf5);
fclose(pf6);
fclose(fsize);
}
