public MetabolicReaction parseTwoSidedReaction(
PreparsedReaction preparsed, String[] equationSides) throws UnparsableReactionError {
Matcher reactionCompartment = REACTION_COMPARTMENT.matcher(equationSides[0]);
MetabolicReaction rxn = getReaction(preparsed);
Compartment defaultCompartment = Organelle.CYTOPLASM;
if (reactionCompartment.find()) {
defaultCompartment = resolver.getCompartment(reactionCompartment.group(1));
equationSides[0] = reactionCompartment.replaceAll("");
}
for (MetabolicParticipantImplementation p :
parseParticipants(equationSides[0], defaultCompartment, preparsed)) {
rxn.addReactant(p);
}
for (MetabolicParticipantImplementation p :
parseParticipants(equationSides[1], defaultCompartment, preparsed)) {
rxn.addProduct(p);
}
return rxn;
}
/** @inheritDoc */
public boolean update(Collection<MetabolicReaction> reactions) {
boolean changed = false;
for (MetabolicReaction reaction : reactions) {
if (reactionMap.containsEntry(reaction.getIdentifier(), reaction)) {
changed = update(reaction) || changed;
}
}
return changed;
}
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);
}
/** Only have left side (or some weird reaction operator) */
public MetabolicReaction parseExchangeReaction(PreparsedReaction reaction, String equationSide)
throws UnparsableReactionError {
Matcher reactionCompartment = REACTION_COMPARTMENT.matcher(equationSide);
MetabolicReaction rxn = getReaction(reaction);
Compartment defaultCompartment = Organelle.CYTOPLASM;
if (reactionCompartment.find()) {
defaultCompartment = resolver.getCompartment(reactionCompartment.group(1));
equationSide = reactionCompartment.replaceAll("");
}
for (MetabolicParticipantImplementation p :
parseParticipants(equationSide, defaultCompartment, reaction)) {
rxn.addReactant(p);
}
return 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;
}
public MetabolicReaction getReaction(PreparsedReaction preparsed) {
MetabolicReaction rxn =
factory.ofClass(
MetabolicReaction.class,
BasicReactionIdentifier.nextIdentifier(),
preparsed.hasValue(DESCRIPTION) ? preparsed.getValue(DESCRIPTION) : "",
preparsed.hasValue(ABBREVIATION) ? preparsed.getValue(ABBREVIATION) : "");
if (preparsed.hasValue(DIRECTION)) {
rxn.setDirection(getReactionArrow(preparsed.getValue(DIRECTION)));
} else {
rxn.setDirection(getReactionArrow(preparsed.getEquation()));
}
// add subsytem annotation
if (preparsed.hasValue(SUBSYSTEM)) {
rxn.addAnnotation(new Subsystem(preparsed.getSubsystem()));
}
// add classification
for (String classification : preparsed.getClassifications()) {
// load EC code
if (classification.matches("(?:\\d+\\.){3}\\d+") || classification.contains("EC")) {
rxn.addAnnotation(new EnzymeClassification(new ECNumber(classification)));
} else if (classification.contains("TC")) {
rxn.addAnnotation(new Classification(new TransportClassificationNumber(classification)));
}
}
// add loci
for (String locus : preparsed.getLoci()) {
rxn.addAnnotation(new Locus(locus));
}
// add delta g and delta g error
if (preparsed.hasValue(FREE_ENERGY)) {
try {
if (preparsed.hasValue(FREE_ENERGY_ERROR)) {
rxn.addAnnotation(
new GibbsEnergy(
Double.parseDouble(preparsed.getValue(FREE_ENERGY)),
Double.parseDouble(preparsed.getValue(FREE_ENERGY_ERROR))));
} else {
rxn.addAnnotation(
new GibbsEnergy(Double.parseDouble(preparsed.getValue(FREE_ENERGY)), 0d));
}
} catch (NumberFormatException ex) {
LOGGER.error("Gibbs energy column(s) contained invalid value (not a double)");
}
}
if (preparsed.hasValue(MIN_FLUX)) {
try {
rxn.addAnnotation(new FluxLowerBound(Double.parseDouble(preparsed.getValue(MIN_FLUX))));
} catch (NumberFormatException ex) {
LOGGER.error(
"Min flux column contained invalid value (not a double): "
+ preparsed.getValue(MIN_FLUX));
}
}
if (preparsed.hasValue(MAX_FLUX)) {
try {
rxn.addAnnotation(new FluxLowerBound(Double.parseDouble(preparsed.getValue(MAX_FLUX))));
} catch (NumberFormatException ex) {
LOGGER.error(
"Max flux column contained invalid value (not a double): "
+ preparsed.getValue(MAX_FLUX));
}
}
return rxn;
}