public void rebuildMaps() {
participantMap.clear();
reactionMap.clear();
for (MetabolicReaction rxn : this) {
for (MetabolicParticipant m : rxn.getReactants()) {
participantMap.get(m.getMolecule().getIdentifier()).add(rxn);
}
for (MetabolicParticipant m : rxn.getProducts()) {
participantMap.get(m.getMolecule().getIdentifier()).add(rxn);
}
reactionMap.put(rxn.getIdentifier(), rxn);
}
}
@Override
public boolean remove(MetabolicReaction rxn) {
// remove links to metabolites
for (MetabolicParticipant p : rxn.getParticipants()) {
Metabolite m = p.getMolecule();
participantMap.get(m.getIdentifier()).remove(rxn);
if (participantMap.get(m.getIdentifier()).isEmpty()) {
participantMap.removeAll(m.getIdentifier());
}
}
reactionMap.remove(rxn.getIdentifier(), rxn);
return super.remove(rxn);
}
@Override
public boolean add(MetabolicReaction rxn) {
if (rxn == null) return false;
if (reactionMap.containsKey(rxn.getIdentifier())) return false;
for (MetabolicParticipant m : rxn.getParticipants()) {
participantMap.get(m.getMolecule().getIdentifier()).add(rxn);
}
reactionMap.put(rxn.getIdentifier(), rxn);
return super.add(rxn);
}
/** @inheritDoc */
public boolean update(MetabolicReaction reaction) {
Identifier identifier = reaction.getIdentifier();
if (reactionMap.containsKey(identifier)) {
PARTICIPANTS:
for (MetabolicParticipant p : reaction.getParticipants()) {
Identifier id = p.getMolecule().getIdentifier();
boolean found = false;
for (MetabolicReaction rxn : participantMap.get(id)) {
if (rxn == reaction) continue PARTICIPANTS; // continue to next participant
}
participantMap.put(id, reaction);
}
return true;
}
return false;
}