END_TEST
/**
* setMathFromFormula() is no longer necessary. LibSBML now keeps formula
* strings and math ASTs synchronized automatically. This (now modified)
* test is kept around to demonstrate the behavioral change.
*/
START_TEST (test_KineticLaw_setMathFromFormula)
{
const char *initial_formula = "k3 / k2";
char* formula;
fail_unless( !KineticLaw_isSetMath (kl) );
fail_unless( !KineticLaw_isSetFormula(kl) );
KineticLaw_setFormula(kl, initial_formula);
fail_unless( KineticLaw_isSetMath (kl) );
fail_unless( KineticLaw_isSetFormula(kl) );
formula = SBML_formulaToString( KineticLaw_getMath(kl) );
fail_unless( !strcmp(formula, initial_formula) );
safe_free(formula);
}
END_TEST
START_TEST (test_KineticLaw_setFormula)
{
const char *formula = "k1*X0";
KineticLaw_setFormula(kl, formula);
fail_unless( !strcmp(KineticLaw_getFormula(kl), formula) );
fail_unless( KineticLaw_isSetFormula(kl) );
if (KineticLaw_getFormula(kl) == formula)
{
fail("KineticLaw_setFormula(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
KineticLaw_setFormula(kl, KineticLaw_getFormula(kl));
fail_unless( !strcmp(KineticLaw_getFormula(kl), formula) );
KineticLaw_setFormula(kl, NULL);
fail_unless( !KineticLaw_isSetFormula(kl) );
if (KineticLaw_getFormula(kl) != NULL)
{
fail("KineticLaw_setFormula(kl, NULL) did not clear string.");
}
}
END_TEST
START_TEST (test_KineticLaw_setFormula2)
{
int i = KineticLaw_setFormula(kl, NULL);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( !KineticLaw_isSetFormula(kl) );
}
END_TEST
START_TEST (test_KineticLaw_setFormula3)
{
char *formula = "k1 X0";
int i = KineticLaw_setFormula(kl, formula);
fail_unless( i == LIBSBML_INVALID_OBJECT);
fail_unless( !KineticLaw_isSetFormula(kl) );
}
END_TEST
START_TEST (test_KineticLaw_setBadFormula)
{
const char *formula = "k1 X0";
KineticLaw_setFormula(kl, formula);
fail_unless( !KineticLaw_isSetFormula(kl) );
fail_unless( !KineticLaw_isSetMath(kl) );
}
END_TEST
/**
* setFormulaFromMath() is no longer necessary. LibSBML now keeps formula
* strings and math ASTs synchronized automatically. This (now modified)
* test is kept around to demonstrate the behavioral change.
*/
START_TEST (test_KineticLaw_setFormulaFromMath)
{
ASTNode_t *math = SBML_parseFormula("k1 * X0");
fail_unless( !KineticLaw_isSetMath (kl) );
fail_unless( !KineticLaw_isSetFormula(kl) );
KineticLaw_setMath(kl, math);
fail_unless( KineticLaw_isSetMath(kl) );
fail_unless( KineticLaw_isSetFormula(kl) );
fail_unless( !strcmp(KineticLaw_getFormula(kl), "k1 * X0") );
ASTNode_free(math);
}
/**
* \fn void SBML_setReactions(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
* \author Amine Ghozlane
* \brief Alloc memory and initialize the struct Especes
* \param mod Model of the SBML file
* \param molecules Struct Especes
* \param result Struct Score
* \param reactions_ratio List of computed reaction ratio
* \param nbReactions Number of reaction
* \param nbEspeces Number of molecules
*/
void SBML_setReactions(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
{
/* Initialisation les reactions auquelles participent chaque espece */
int ref = 0, i, j, resultat=OK;
SpeciesReference_t *reactif=NULL;
Species_t *especeId=NULL;
Reaction_t *react=NULL;
const char *kf=NULL;
/*const ASTNode_t *km;*/
KineticLaw_t *kl=NULL;
/* Recherche les reactions ou apparaissent chaque espece */
for (i = 0; i < nbReactions; i++) {
react = Model_getReaction(mod, i);
/* Recherche si la reaction est etudiee */
resultat = SBML_findReaction(result->reaction,Reaction_getId(react), result->nb_reaction);
/* Etude des reactifs */
for (j = 0; j < (int)Reaction_getNumReactants(react); j++) {
/* Recuperation d'un reactif */
reactif = Reaction_getReactant(react, j);
/* Recuperation du nom de l'espece */
especeId = Model_getSpeciesById(mod, SpeciesReference_getSpecies(reactif));
/* Recherche la reference de cette molecule dans la struture molecule */
ref = Especes_find(molecules, Species_getId(especeId), nbEspeces);
/* Recuperation de la loi cinetique sur la */
kl = Reaction_getKineticLaw(react);
/* Reaction dont on recherche le bon ratio */
if(resultat!=OK){
Especes_allocReactions(molecules, ref, react, reactions_ratio[resultat]);
}
/* Si la loi cinetique est au format : formule on recupere le ratio en question */
else if (KineticLaw_isSetFormula(kl)) {
kf = KineticLaw_getFormula(kl);
Especes_allocReactions(molecules, ref, react, SBML_evalExpression(kf));
} else { /* Sinon on n'utilise pas ces informations */
/*km = KineticLaw_getMath(kl);*/
fprintf(stderr,"SBML equation are taken into account, use instead the parameter file\n");
/*exit(EXIT_FAILURE);*/
}
}
}
}
/**
* \fn void SBML_score(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
* \author Amine Ghozlane
* \brief Alloc memory and initialize the struct Especes
* \param mod Model of the SBML file
* \param molecules Struct Especes
* \param result Struct Score
* \param reactions_ratio List of computed reaction ratio
* \param nbReactions Number of reactions
* \param nbEspeces Number of molecules
*/
void SBML_score(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
{
/* Fonction de score */
int i, resultat=OK;
Reaction_t *react=NULL;
const char *kf=NULL;
KineticLaw_t *kl=NULL;
/* Enregistre le score des especes */
Especes_scoreSpecies(molecules, nbEspeces, result->name, result->quantite);
/* Enregistre le ratio des reactions */
for (i = 0; i < (nbReactions); i++) {
react = Model_getReaction(mod, i);
if(result->name[nbEspeces+i]==NULL){
result->name[nbEspeces+i]=(char*)malloc(((int)strlen((char *)Reaction_getId(react))+1)*sizeof(char));
assert(result->name[nbEspeces+i]!=NULL);
strcpy(result->name[nbEspeces+i],(char *)Reaction_getId(react));
}
/* Recherche si la reaction est etudiee*/
resultat = SBML_findReaction(result->reaction, result->name[nbEspeces+i], result->nb_reaction);
/* Recuperation de la loi cinetique sur la */
kl = Reaction_getKineticLaw(react);
/* Reaction dont on recherche le bon ratio*/
if(resultat!=OK) result->quantite[nbEspeces+i]=reactions_ratio[resultat];
else if(KineticLaw_isSetFormula(kl)){
kf = KineticLaw_getFormula(kl);
result->quantite[nbEspeces+i]=SBML_evalExpression(kf);
}
else { /*Sinon on n'utilise pas ces informations*/
fprintf(stderr,"SBML equation are taken into account, use instead the parameter file\n");
exit(EXIT_FAILURE);
}
}
}