+ vector<string> Groups = m->getGroups();
+ vector<string> allGroups = groupmap->getNamesOfGroups();
+ util->setGroups(Groups, allGroups);
+ m->setGroups(Groups);
+ delete util;
+
+ for (int i = 0; i < allGroups.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector(data.size());
+ finder[allGroups[i]] = temp;
+ finder[allGroups[i]]->setLabel(label);
+ finder[allGroups[i]]->setGroup(allGroups[i]);
+ if (m->inUsersGroups(allGroups[i], m->getGroups())) { //if this group is in user groups
+ lookup.push_back(finder[allGroups[i]]);
+ }
+ }
+
+ //fill vectors
+ for(int i=0;i<numBins;i++){
+ names = get(i);
+ int nameLength = names.size();
+ string seqName = "";
+
+ for(int j=0;j<nameLength;j++){
+ if(names[j] == ','){
+ group = groupmap->getGroup(seqName);
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+ finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
+
+ seqName = "";
+ }
+ else{
+ seqName += names[j];
+ }
+ }
+ group = groupmap->getGroup(seqName);
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+ finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
+
+
+
+// while (names.find_first_of(',') != -1) {
+// name = names.substr(0,names.find_first_of(','));
+// names = names.substr(names.find_first_of(',')+1, names.length());
+// group = groupmap->getGroup(name);
+// if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+// finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
+// }
+
+ //get last name
+// group = groupmap->getGroup(names);
+// if(group == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+// finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
+