added groups option to read.otu, added qtrim option to trim.seqs, fixed bug in get...

[mothur.git] / sharedlistvector.cpp

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index a113ebe7e82e93f135541b0bfa0ffc7a3b1d33b1..6cac9b1d9512a16d15eef553d351de0b16771b6e 100644 (file)
--- 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");