X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedlistvector.cpp;fp=sharedlistvector.cpp;h=6cac9b1d9512a16d15eef553d351de0b16771b6e;hb=f5023c911c377e5320c5110c78af98dd8841ef58;hp=a113ebe7e82e93f135541b0bfa0ffc7a3b1d33b1;hpb=3c856e629e20261496b0433c2587f27b2c8ba3f6;p=mothur.git

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index a113ebe..6cac9b1 100644
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -264,22 +264,23 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
 		SharedUtil* util;
 		util = new SharedUtil();
 		vector<SharedRAbundVector*> lookup;
+		vector<SharedRAbundVector*> lookup2;
 		map<string, SharedRAbundVector*> finder;
+		map<string, SharedRAbundVector*>::iterator it;
 		string group, names, name;
-		
+	
 		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
-		
 		delete util;
 
-		for (int i = 0; i < globaldata->Groups.size(); i++) {
+		for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 			SharedRAbundVector* temp = new SharedRAbundVector(data.size());
-			finder[globaldata->Groups[i]] = temp;
-			finder[globaldata->Groups[i]]->setLabel(label);
-			finder[globaldata->Groups[i]]->setGroup(globaldata->Groups[i]);
+			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->Groups[i]]);
+			lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
 		}
-		
+//cout << "after blanks" << endl;		
 		//fill vectors
 		for(int i=0;i<numBins;i++){
 			names = get(i);  
@@ -287,18 +288,30 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
 				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
 			
 		}
 		
-		return lookup;
+		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;
 	}
 	catch(exception& e) {
 		errorOut(e, "SharedListVector", "getSharedRAbundVector");