changed how we do "smart" distancing

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 4ae8e244031a5ea194724fcb4581bbd677e4bc9c..e8fb553e42a3ca655b2e8b063c359d7cad4968f9 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -195,7 +195,7 @@ int MatrixOutputCommand::execute(){
                        
                input = globaldata->ginput;
                lookup = input->getSharedRAbundVectors();
-               vector<SharedRAbundVector*> lastLookup = lookup;
+               string lastLabel = lookup[0]->getLabel();
                
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
@@ -218,19 +218,23 @@ int MatrixOutputCommand::execute(){
                                userLines.erase(count);
                        }
                        
-                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
-                               cout << lastLookup[0]->getLabel() << '\t' << count << endl;
-                               process(lastLookup);
+                       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;
+                               process(lookup);
                                
-                               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++;
                }
@@ -240,23 +244,25 @@ int MatrixOutputCommand::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;
-                       process(lastLookup);            
-               }
-               
-               for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
+                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+                       lookup = input->getSharedRAbundVectors(lastLabel);
 
+                       cout << lookup[0]->getLabel() << '\t' << count << endl;
+                       process(lookup);
+                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+               }
                
+                               
                //reset groups parameter
                globaldata->Groups.clear();