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

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 582628d8f6a98151efb9a525bf9cdc26383be379..fd28e841faee71bf35ed49a3f6ff21e4455cb8fa 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -42,6 +42,7 @@ CollectSharedCommand::CollectSharedCommand(){
                string fileNameRoot;
                fileNameRoot = getRootName(globaldata->inputFileName);
                format = globaldata->getFormat();
+               convert(globaldata->getFreq(), freq);
                validCalculator = new ValidCalculators();
                util = new SharedUtil();
                
@@ -134,39 +135,74 @@ int CollectSharedCommand::execute(){
                        
                input = globaldata->ginput;
                order = input->getSharedOrderVector();
+               SharedOrderVector* lastOrder = order;
                
-               set<string> orderList;
-               
+               //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;
+                               
                //set users groups
                util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
                util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
-               while(order != NULL){
+               while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 
-                       orderList.insert(order->getLabel());
-                       
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
                                
                                //create collectors curve
                                cCurve = new Collect(order, cDisplays);
-                               convert(globaldata->getFreq(), freq);
                                cCurve->getSharedCurve(freq);
-                       
                                delete cCurve;
                        
                                cout << order->getLabel() << '\t' << count << endl;
+                               processedLabels.insert(order->getLabel());
+                               userLabels.erase(order->getLabel());
+
+                       //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)) {
+                               //create collectors curve
+                               cCurve = new Collect(lastOrder, cDisplays);
+                               cCurve->getSharedCurve(freq);
+                               delete cCurve;
+                       
+                               cout << lastOrder->getLabel() << '\t' << count << endl;
+                               processedLabels.insert(lastOrder->getLabel());
+                               userLabels.erase(lastOrder->getLabel());
                        }
                        
+                       if (count != 1) { delete lastOrder; }
+                       lastOrder = order;                      
+                       
                        //get next line to process
-                       delete order;
                        order = input->getSharedOrderVector();
                        count++;
                }
-               set<string>::iterator i;
-               for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
-                       if(orderList.count(*i) == 0)
-                               cout << "'" << *i << "'" << " is not a valid label.\n";
-                               
+               
+               //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)  {
+                       cCurve = new Collect(lastOrder, cDisplays);
+                       cCurve->getCurve(freq);
+                       delete cCurve;
+                       
+                       cout << lastOrder->getLabel() << '\t' << count << endl;
+               }
+               
+               delete lastOrder;
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
                
                //reset groups parameter