- sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
-
- //initialize bin values
- for (int i = 0; i < thislookup.size(); i++) {
-//cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;
- out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
- thislookup[i]->print(out);
+ if (order.size() == 0) { //user has not specified an order so do aplabetically
+ sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
+
+ //initialize bin values
+ for (int i = 0; i < thislookup.size(); i++) {
+ out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+ thislookup[i]->print(out);
+
+ RAbundVector rav = thislookup[i]->getRAbundVector();
+ openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+ rav.print(*(filehandles[thislookup[i]->getGroup()]));
+ (*(filehandles[thislookup[i]->getGroup()])).close();
+ }
+ }else{
+ //create a map from groupName to each sharedrabund
+ map<string, SharedRAbundVector*> myMap;
+ map<string, SharedRAbundVector*>::iterator myIt;
+
+ for (int i = 0; i < thislookup.size(); i++) {
+ myMap[thislookup[i]->getGroup()] = thislookup[i];
+ }
+