added smart distance feature and optimized all commands using line by line processing

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 981f077969b1e734b2dc39fb05b372daa2a5f455..752ff62298ed183f18e033982b1e0c20513bd963 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -27,6 +27,8 @@ RareFactCommand::RareFactCommand(){
                globaldata = GlobalData::getInstance();
                string fileNameRoot;
                fileNameRoot = getRootName(globaldata->inputFileName);
+               convert(globaldata->getFreq(), freq);
+               convert(globaldata->getIters(), nIters);
                validCalculator = new ValidCalculators();
                
                int i;
@@ -96,28 +98,68 @@ int RareFactCommand::execute(){
                read->read(&*globaldata); 
 
                order = globaldata->gorder;
+               OrderVector* lastOrder = order;
                input = globaldata->ginput;
-       
-               while(order != NULL){
                
+               //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+               set<string> processedLabels;
+               set<string> userLabels = globaldata->labels;
+       
+               //as long as you are not at the end of the file or done wih the lines you want
+               while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+                       
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
                        
                                rCurve = new Rarefact(order, rDisplays);
-                               convert(globaldata->getFreq(), freq);
-                               convert(globaldata->getIters(), nIters);
                                rCurve->getCurve(freq, nIters);
-                       
                                delete rCurve;
                        
                                cout << order->getLabel() << '\t' << count << endl;
+                               processedLabels.insert(order->getLabel());
+                               userLabels.erase(order->getLabel());
+                       }
+                       
+                       if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
+                               rCurve = new Rarefact(lastOrder, rDisplays);
+                               rCurve->getCurve(freq, nIters);
+                               delete rCurve;
+                       
+                               cout << lastOrder->getLabel() << '\t' << count << endl;
+                               processedLabels.insert(lastOrder->getLabel());
+                               userLabels.erase(lastOrder->getLabel());
                        }
                        
-                       delete order;
+                       if (count != 1) { delete lastOrder; }
+                       lastOrder = order;                      
+
                        order = (input->getOrderVector());
                        count++;
+               }
                
+               //output error messages about any remaining user labels
+               set<string>::iterator it;
+               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;
+                               needToRun = true;
+                       }else {
+                               cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+                       }
                }
-       
+               
+               //run last line if you need to
+               if (needToRun == true)  {
+                       rCurve = new Rarefact(lastOrder, rDisplays);
+                       rCurve->getCurve(freq, nIters);
+                       delete rCurve;
+                       
+                       cout << lastOrder->getLabel() << '\t' << count << endl;
+               }
+               
+               delete lastOrder;
+
                for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }       
                return 0;
        }