/**
* Returns a collection of bounds for reactions included in the given's model metabolism. Note
* that it has to be a sum of bounds of the parent model (if the given model has a parent) and the
* bounds directly associated with current model.
*
* @param model
* @return collection of bounds for the given model
*/
Collection<EBounds> getBoundsForModel(EModel model, EntityManager em) {
if (model.getParent() == null) {
return model.getEBoundsCollection();
} else {
/*
* There are two sources of bounds for each model.
* First, we retrieve bounds that have been defined for this model
*/
List<EBounds> res1 =
em.createQuery("SELECT e FROM EBounds e WHERE e.model = :model")
.setParameter("model", model)
.getResultList();
/*
* The remaining bounds are taken from the parent model
*/
List<EBounds> res2 =
em.createQuery(
" SELECT b FROM EModel m, EBounds b WHERE "
+ " m.id = :modelID AND m.parent IS NOT NULL AND "
+ " b.model = m.parent AND NOT EXISTS (SELECT c "
+ " FROM EBounds c WHERE c.model = :model AND "
+ " b.reaction = c.reaction )")
.setParameter("modelID", model.getId())
.setParameter("model", model)
.getResultList();
res1.addAll(res2);
return res1;
}
}
/**
* Returns list of all models from database that are ancestors of a given model (transitive
* closure version).
*
* @return - list of all ancestors of a given model (including that model).
*/
public List<EModel> getAncestorsModels(EModel start) {
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
// List<EModel> allModels = (List<EModel>) em.createQuery("select m from EModel as
// m").getResultList();
EModel model = start;
List<EModel> result = new LinkedList<EModel>();
// assume that the start model is really a model from the database
result.add(model);
// transitive closure
while (model.getParent() != null) {
result.add(model.getParent());
model = model.getParent();
}
em.getTransaction().commit();
return result;
} finally {
em.close();
}
}
