try {
SharedUtil* util;
util = new SharedUtil();
- vector<SharedRAbundVector*> lookup;
- vector<SharedRAbundVector*> lookup2;
- map<string, SharedRAbundVector*> finder;
- map<string, SharedRAbundVector*>::iterator it;
+ vector<SharedRAbundVector*> lookup; //contains just the groups the user selected
+ map<string, SharedRAbundVector*> finder; //contains all groups in groupmap
string group, names, name;
util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
finder[globaldata->gGroupmap->namesOfGroups[i]] = temp;
finder[globaldata->gGroupmap->namesOfGroups[i]]->setLabel(label);
finder[globaldata->gGroupmap->namesOfGroups[i]]->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
- //*temp = getSharedRAbundVector(globaldata->Groups[i]);
- lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
+ if (inVector(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) { //if this group is in user groups
+ lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
+ }
}
-//cout << "after blanks" << endl;
+
//fill vectors
for(int i=0;i<numBins;i++){
names = get(i);
name = names.substr(0,names.find_first_of(','));
names = names.substr(names.find_first_of(',')+1, names.length());
group = groupmap->getGroup(name);
-//cout << i << '\t' << name << '\t' << group << endl;
if(group == "not found") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); 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);
-//cout << i << '\t' << names << '\t' << group << endl;
if(group == "not found") { mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
}
- if (globaldata->Groups.size() == globaldata->gGroupmap->namesOfGroups.size()) { //no groups specified
- lookup2 = lookup;
- }else{ //delete unwanted groups
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(*finder[globaldata->Groups[i]]);
- lookup2.push_back(temp);
- delete finder[globaldata->Groups[i]]; //so we don't get dup memory
- }
- }
-
- return lookup2;
+ return lookup;
}
catch(exception& e) {
errorOut(e, "SharedListVector", "getSharedRAbundVector");