@Override
protected void processMethodAndType(
EncoreInteraction encoreInteraction, EncoreInteraction mappingEncoreInteraction) {
Map<MethodTypePair, List<String>> existingMethodTypeToPubmed =
mappingEncoreInteraction.getMethodTypePairListMap();
for (Map.Entry<MethodTypePair, List<String>> entry :
encoreInteraction.getMethodTypePairListMap().entrySet()) {
if (existingMethodTypeToPubmed.containsKey(entry.getKey())) {
List<String> existingPubmeds = existingMethodTypeToPubmed.get(entry.getKey());
List<String> newPubmeds = encoreInteraction.getMethodTypePairListMap().get(entry.getKey());
for (String pub : newPubmeds) {
if (!existingPubmeds.contains(pub)) {
existingPubmeds.add(pub);
}
}
} else {
existingMethodTypeToPubmed.put(entry.getKey(), entry.getValue());
}
}
}
@Override
protected EncoreInteraction mergeWithExistingEncoreInteraction(
EncoreInteraction encoreInteraction, int interactionIdFound) {
EncoreInteraction
mappingEcoreInteraction; // include additional information about exp, pubmed, ... for this
// interaction id
mappingEcoreInteraction = interactionMapping.get(interactionIdFound);
if (mappingEcoreInteraction == null) {
throw new IllegalStateException(
"Could not find an EncoreInteraction with id: " + interactionIdFound);
}
/* Check that interactors are in the same order A=A and B=B */
boolean swapInteractors = true;
swap_loop:
for (String acc : mappingEcoreInteraction.getInteractorAccsA().values()) {
if (encoreInteraction.getInteractorAccsA().containsValue(acc)) {
swapInteractors = false;
break swap_loop;
}
}
if (swapInteractors) {
mappingEcoreInteraction.addInteractorAccsA(encoreInteraction.getInteractorAccsB());
mappingEcoreInteraction.addInteractorAccsB(encoreInteraction.getInteractorAccsA());
mappingEcoreInteraction.addOtherInteractorAccsA(encoreInteraction.getOtherInteractorAccsB());
mappingEcoreInteraction.addOtherInteractorAccsB(encoreInteraction.getOtherInteractorAccsA());
mappingEcoreInteraction.addOrganismsA(encoreInteraction.getOrganismsB());
mappingEcoreInteraction.addOrganismsB(encoreInteraction.getOrganismsA());
} else {
mappingEcoreInteraction.addInteractorAccsA(encoreInteraction.getInteractorAccsA());
mappingEcoreInteraction.addInteractorAccsB(encoreInteraction.getInteractorAccsB());
mappingEcoreInteraction.addOtherInteractorAccsA(encoreInteraction.getOtherInteractorAccsA());
mappingEcoreInteraction.addOtherInteractorAccsB(encoreInteraction.getOtherInteractorAccsB());
mappingEcoreInteraction.addOrganismsA(encoreInteraction.getOrganismsA());
mappingEcoreInteraction.addOrganismsB(encoreInteraction.getOrganismsB());
}
mappingEcoreInteraction.addPublicationId(encoreInteraction.getPublicationIds());
mappingEcoreInteraction.addExperimentToPubmed(encoreInteraction.getExperimentToPubmed());
mappingEcoreInteraction.addExperimentToDatabase(encoreInteraction.getExperimentToDatabase());
processMethodAndType(encoreInteraction, mappingEcoreInteraction);
mappingEcoreInteraction.addAuthors(encoreInteraction.getAuthors());
mappingEcoreInteraction.addConfidenceValues(encoreInteraction.getConfidenceValues());
mappingEcoreInteraction.addSourceDatabases(encoreInteraction.getSourceDatabases());
mappingEcoreInteraction
.getDistinctPublications()
.addAll(encoreInteraction.getDistinctPublications());
return mappingEcoreInteraction;
}