public void addModel(
EMetabolism metabolism,
EModel model,
Map<String, ECompartment> compartment_map,
Map<String, ESpecies> species_map,
List<EReaction> reaction_list,
List<EReactant> reactant_list,
List<EProduct> product_list,
List<EBounds> bounds_list) {
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
em.persist(metabolism);
em.persist(model);
model.getMetabolism().getEModelCollection().add(model);
for (ECompartment c : compartment_map.values()) {
em.persist(c);
c.getMetabolism().getECompartmentCollection().add(c);
}
for (ESpecies sp : species_map.values()) {
em.persist(sp);
sp.getCompartment().getESpeciesCollection().add(sp);
}
for (EReaction r : reaction_list) {
em.persist(r);
r.getMetabolism().getEReactionCollection().add(r);
}
for (EReactant r : reactant_list) {
em.persist(r);
r.getSpecies().getEReactantCollection().add(r);
/* r.getReaction().getEReactantCollection().add(r); */
}
for (EProduct p : product_list) {
em.persist(p);
p.getSpecies().getEProductCollection().add(p);
/* p.getReaction().getEProductCollection().add(p); */
}
for (EBounds b : bounds_list) {
em.persist(b);
b.getModel().getEBoundsCollection().add(b);
/* b.getReaction().getEBoundsCollection().add(b); */
}
em.merge(metabolism);
em.getTransaction().commit();
} finally {
em.close();
}
}
/** Removes @bounds. */
public void removeBounds(EModel model) {
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
for (EBounds bounds : model.getEBoundsCollection()) {
EBounds boundsx = em.find(EBounds.class, bounds.getId());
em.remove(boundsx);
}
em.getTransaction().commit();
} finally {
em.close();
}
}
/**
* @param modelId
* @return creactions
*/
public Collection<EReaction> getDetachedReactions(int modelId) {
ArrayList<EReaction> detachedReactions = new ArrayList<EReaction>(0);
EModel model = getModel(modelId);
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
Collection<EBounds> eboundColl = model.getEBoundsCollection();
for (EBounds bounds : eboundColl) {
if (bounds.getLowerBound() == 0 && bounds.getUpperBound() == 0) {
detachedReactions.add(bounds.getReaction());
}
}
em.getTransaction().commit();
} catch (NoResultException ex) {
em.getTransaction().rollback();
} finally {
em.close();
}
return detachedReactions;
}
