fixed phylo.diversity

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 2c1b6af3004e7351085e4538f7023e342bc181f9..fb3691e662a7ee2b378d8e1dd13e4221b698106d 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -259,6 +259,7 @@ int SharedCommand::execute(){
                globaldata->setGroupFile("");
                globaldata->setSharedFile(filename);
                
+               
                if (m->control_pressed) { 
                                delete input;  globaldata->ginput = NULL; 
                                remove(filename.c_str()); 
@@ -286,11 +287,15 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
                if (order.size() == 0) { //user has not specified an order so do aplabetically
                        sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
                        
+                       globaldata->Groups.clear();
+                       
                        //initialize bin values
                        for (int i = 0; i < thislookup.size(); i++) {
                                out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
                                thislookup[i]->print(out);
                                
+                               globaldata->Groups.push_back(thislookup[i]->getGroup());
+                               
                                RAbundVector rav = thislookup[i]->getRAbundVector();
                                m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
                                rav.print(*(filehandles[thislookup[i]->getGroup()]));
@@ -305,6 +310,7 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
                                myMap[thislookup[i]->getGroup()] = thislookup[i];
                        }
                        
+                       globaldata->Groups.clear();
                        
                        //loop through ordered list and print the rabund
                        for (int i = 0; i < order.size(); i++) {
@@ -313,6 +319,8 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
                                if(myIt != myMap.end()) { //we found it
                                        out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
                                        (myIt->second)->print(out);
+                                       
+                                       globaldata->Groups.push_back((myIt->second)->getGroup());
                                
                                        RAbundVector rav = (myIt->second)->getRAbundVector();
                                        m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));