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;
}
@Test
public void testAddProduct_Metabolite() throws Exception {
MetabolicReaction mock = mock(MetabolicReaction.class);
MetabolicReaction rxn = new BiochemRxnImpl(mock);
Metabolite m = mock(Metabolite.class);
rxn.addProduct(m);
verify(mock).addProduct(m);
}
@Test
public void testAddProduct() throws Exception {
MetabolicReaction mock = mock(MetabolicReaction.class);
MetabolicReaction rxn = new BiochemRxnImpl(mock);
MetabolicParticipant p = mock(MetabolicParticipant.class);
rxn.addProduct(p);
verify(mock).addProduct(p);
}
