Added get.line command.

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 0f622c49b2a30632f53e4fa3ec0dfc3196113374..f012ba151e0813f9b7ab67f5c2961db8eec23b1b 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -36,6 +36,7 @@ CollectCommand::CollectCommand(){
                                }else if (globaldata->Estimators[i] == "chao") { 
                                        cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
                                }else if (globaldata->Estimators[i] == "ace") { 
+                               convert(globaldata->getAbund(), abund);
                                        cDisplays.push_back(new CollectDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"ace")));
                                }else if (globaldata->Estimators[i] == "jack") { 
                                        cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
@@ -88,11 +89,12 @@ int CollectCommand::execute(){
                
                order = globaldata->gorder;
                input = globaldata->ginput;
-                       
+               set<string> orderList;  
+               
                while(order != NULL){
                
+                       orderList.insert(order->getLabel());
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
-                       
                                cCurve = new Collect(order, cDisplays);
                                convert(globaldata->getFreq(), freq);
                                cCurve->getCurve(freq);
@@ -101,12 +103,14 @@ int CollectCommand::execute(){
                        
                                cout << order->getLabel() << '\t' << count << endl;
                        }
-               
                        order = (input->getOrderVector());
                        count++;
-               
                }
-       
+               set<string>::iterator i;
+               for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
+                       if(orderList.count(*i) == 0)
+                               cout << "'" << *i << "'" << " is not a valid label.\n";
+               globaldata->clearLabels();
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
                return 0;
        }