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 void loadNetwork() throws IOException {
logger.log(Level.INFO, "Loading metabolism network...");
File file = props.getNetworkFile();
Mapper<String, MetabolicEntry> entryMapper = new MetabolicEntry.MetabolicMapper();
Parser<MetabolicEntry> parser = new Parser<MetabolicEntry>(file, entryMapper);
while (parser.hasNext()) {
MetabolicEntry entry = parser.next();
entries.add(entry);
Rxn rxn =
new Rxn(
props,
entry.getReaction(),
entry.getAbbreviation(),
entry.getReactionName(),
entry.getORF());
reactions.put(entry.getAbbreviation(), rxn);
locations.add(rxn.getLocation());
LogicalORFTree lot = new LogicalORFTree(entry.getORF());
ORFSet os = new ORFSet(entry.getORF());
totalORFs.addAll(os.getORFs());
orfSets.put(entry.getAbbreviation(), lot);
}
logger.log(Level.FINE, String.format("Loaded %d entries.", entries.size()));
abbrevs = new MetabolismAbbreviations(props);
abbrevs.loadAbbreviations();
logger.log(Level.FINEST, "Loaded abbrevations.");
}
public Set<String> getReactionAbbreviations() {
return reactions.keySet();
}
public Rxn getReaction(String rxnAbbrev) {
return reactions.get(rxnAbbrev);
}
public LogicalORFTree getLogicalORFTree(String rxnAbbrev) {
return orfSets.get(rxnAbbrev);
}