changed how we do "smart" distancing

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 1e10736f281b76f59c0e74374ba1b8afd4d36646..f5beb32b6a8296411dcd66afa18efc6b3be24577 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -124,7 +124,7 @@ int GetSAbundCommand::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.
@@ -147,20 +147,24 @@ int GetSAbundCommand::execute(){
                                        userLines.erase(count);
                        }
                        
-                       if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
-                                       cout << lastOrder->getLabel() << '\t' << count << endl;
+                       if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                                       delete order;           
+                                       order = (input->getOrderVector(lastLabel));
+                                       
+                                       cout << order->getLabel() << '\t' << count << endl;
                                        sabund = new SAbundVector();
-                                       *sabund = (lastOrder->getSAbundVector());
+                                       *sabund = (order->getSAbundVector());
                                        sabund->print(out);
                                        delete sabund;
 
-                                       processedLabels.insert(lastOrder->getLabel());
-                                       userLabels.erase(lastOrder->getLabel());
+                                       processedLabels.insert(order->getLabel());
+                                       userLabels.erase(order->getLabel());
                        }
                        
-                       if (count != 1) { delete lastOrder; }
-                       lastOrder = order;      
-                                       
+                       
+                       lastLabel = order->getLabel();  
+                       
+                       delete order;           
                        order = (input->getOrderVector());
                        count++;
                }
@@ -170,23 +174,27 @@ int GetSAbundCommand::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)  {
-                       cout << lastOrder->getLabel() << '\t' << count << endl;
+                       delete order;           
+                       order = (input->getOrderVector(lastLabel));
+                       
+                       cout << order->getLabel() << '\t' << count << endl;
                        sabund = new SAbundVector();
-                       *sabund = (lastOrder->getSAbundVector());
+                       *sabund = (order->getSAbundVector());
                        sabund->print(out);
                        delete sabund;
+                       delete order;
                }
-               delete lastOrder;  globaldata->gorder = NULL;
+               globaldata->gorder = NULL;
 
                out.close();
                return 0;