/** Merge identified modified compounds if linked. */
private void mergeModComps(List<ModifiedCompound> modComps) {
TreeSet<Integer> remove = new TreeSet<Integer>();
int n = modComps.size();
for (int icurr = 1; icurr < n; icurr++) {
ModifiedCompound curr = modComps.get(icurr);
String id = curr.getModification().getId();
if (ProteinModificationRegistry.getById(id).getCategory() != ModificationCategory.UNDEFINED)
continue;
// find linked compounds that before curr
// List<Integer> merging = new ArrayList<Integer>();
int ipre = 0;
for (; ipre < icurr; ipre++) {
if (remove.contains(ipre)) continue;
ModifiedCompound pre = modComps.get(ipre);
if (!Collections.disjoint(pre.getGroups(false), curr.getGroups(false))) {
break;
}
}
if (ipre < icurr) {
ModifiedCompound mcKeep = modComps.get(ipre);
// merge modifications of the same type
if (mcKeep.getModification().getId().equals(id)) {
// merging the current one to the previous one
mcKeep.addAtomLinkages(curr.getAtomLinkages());
remove.add(icurr);
}
}
}
Iterator<Integer> it = remove.descendingIterator();
while (it.hasNext()) {
modComps.remove(it.next().intValue());
}
}
