public Map<String, Rxn> getReactions(String compartment) {
TreeMap<String, Rxn> crxns = new TreeMap<String, Rxn>();
for (String rn : reactions.keySet()) {
Rxn r = reactions.get(rn);
if (r.getLocation().equals(compartment)) {
crxns.put(rn, r);
}
}
return crxns;
}
public Set<String> getOutputReactions(Rxn r) {
TreeSet<String> rxns = new TreeSet<String>();
for (String rn : reactions.keySet()) {
Rxn rxn = reactions.get(rn);
if (r.connects(rxn)) {
rxns.add(rn);
}
}
return rxns;
}
public Rxn getReaction(String rxnAbbrev) {
return reactions.get(rxnAbbrev);
}
public LogicalORFTree getLogicalORFTree(String rxnAbbrev) {
return orfSets.get(rxnAbbrev);
}