changed how we do "smart" distancing

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 6461b3bc22922af68cba684893eb00f76e35a598..d527f8b87af8ab1b29537af212d7229d2e70a75b 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -178,7 +178,7 @@ int RareFactSharedCommand::execute(){
                        
                input = globaldata->ginput;
                lookup = input->getSharedRAbundVectors();
-               vector<SharedRAbundVector*> lastLookup = lookup;
+               string lastLabel = lookup[0]->getLabel();
 
                if (lookup.size() < 2) { 
                        cout << "I cannot run the command without at least 2 valid groups."; 
@@ -206,21 +206,24 @@ int RareFactSharedCommand::execute(){
                                userLines.erase(count);
                        }
                        
-                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
-                                       cout << lastLookup[0]->getLabel() << '\t' << count << endl;
-                                       rCurve = new Rarefact(lastLookup, rDisplays);
+                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+                                       lookup = input->getSharedRAbundVectors(lastLabel);
+
+                                       cout << lookup[0]->getLabel() << '\t' << count << endl;
+                                       rCurve = new Rarefact(lookup, rDisplays);
                                        rCurve->getSharedCurve(freq, nIters);
                                        delete rCurve;
 
-                                       processedLabels.insert(lastLookup[0]->getLabel());
-                                       userLabels.erase(lastLookup[0]->getLabel());
+                                       processedLabels.insert(lookup[0]->getLabel());
+                                       userLabels.erase(lookup[0]->getLabel());
                        }
                                
-                       //prevent memory leak
-                       if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
-                       lastLookup = lookup;
+                       
+                       lastLabel = lookup[0]->getLabel();
                        
                        //get next line to process
+                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                        lookup = input->getSharedRAbundVectors();
                        count++;
                }
@@ -230,24 +233,26 @@ int RareFactSharedCommand::execute(){
                bool needToRun = false;
                for (it = userLabels.begin(); it != userLabels.end(); it++) {  
                        cout << "Your file does not include the label "<< *it; 
-                       if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
-                               cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+                       if (processedLabels.count(lastLabel) != 1) {
+                               cout << ". I will use " << lastLabel << "." << endl;
                                needToRun = true;
                        }else {
-                               cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+                               cout << ". Please refer to " << lastLabel << "." << endl;
                        }
                }
                
                //run last line if you need to
                if (needToRun == true)  {
-                       cout << lastLookup[0]->getLabel() << '\t' << count << endl;
-                       rCurve = new Rarefact(lastLookup, rDisplays);
+                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+                       lookup = input->getSharedRAbundVectors(lastLabel);
+
+                       cout << lookup[0]->getLabel() << '\t' << count << endl;
+                       rCurve = new Rarefact(lookup, rDisplays);
                        rCurve->getSharedCurve(freq, nIters);
                        delete rCurve;
+                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                }
                
-               for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
-
                for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }       
                
                //reset groups parameter