changed how we do "smart" distancing

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index c65080fd32022bcd9abb8d3cf10f73de8f181351..dbb2edebb57d76152b570902b4f3b4151bc39d71 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -220,7 +220,7 @@ int CollectCommand::execute(){
                read->read(&*globaldata); 
                
                order = globaldata->gorder;
-               lastOrder = order;
+               string lastLabel = order->getLabel();
                input = globaldata->ginput;
                
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
@@ -244,18 +244,23 @@ int CollectCommand::execute(){
                        //you have a label the user want that is smaller than this line and the last line has not already been processed 
                        }
                        
-                       if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
-                               cCurve = new Collect(lastOrder, cDisplays);
+                       if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                               
+                               delete order;
+                               order = (input->getOrderVector(lastLabel));
+                               
+                               cCurve = new Collect(order, cDisplays);
                                cCurve->getCurve(freq);
                                delete cCurve;
                        
-                               cout << lastOrder->getLabel() << '\t' << count << endl;
-                               processedLabels.insert(lastOrder->getLabel());
-                               userLabels.erase(lastOrder->getLabel());
+                               cout << order->getLabel() << '\t' << count << endl;
+                               processedLabels.insert(order->getLabel());
+                               userLabels.erase(order->getLabel());
                        }
                        
-                       if (count != 1) { delete lastOrder;  }
-                       lastOrder = order;                      
+                       lastLabel = order->getLabel();  
+                       
+                       delete order;           
                        order = (input->getOrderVector());
                        count++;
                }
@@ -265,24 +270,28 @@ int CollectCommand::execute(){
                bool needToRun = false;
                for (it = userLabels.begin(); it != userLabels.end(); it++) {  
                        cout << "Your file does not include the label "<< *it; 
-                       if (processedLabels.count(lastOrder->getLabel()) != 1) {
-                               cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+                       if (processedLabels.count(lastLabel) != 1) {
+                               cout << ". I will use " << lastLabel << "." << endl;
                                needToRun = true;
                        }else {
-                               cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+                               cout << ". Please refer to " << lastLabel << "." << endl;
                        }
                }
                
                //run last line if you need to
                if (needToRun == true)  {
-                       cCurve = new Collect(lastOrder, cDisplays);
+                       delete order;
+                       order = (input->getOrderVector(lastLabel));
+                       
+                       cout << order->getLabel() << '\t' << count << endl;
+                       
+                       cCurve = new Collect(order, cDisplays);
                        cCurve->getCurve(freq);
                        delete cCurve;
-                       
-                       cout << lastOrder->getLabel() << '\t' << count << endl;
+                       delete order;
                }
                
-               delete lastOrder;
+               
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
                return 0;
        }