added get.rabund and get.sabund command and fixed bug introduced by line by line...

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 89cf4e2732af38c6fff844490effde5f8676e76c..c9300259f90726511200a077c9ef633ec7eaa76b 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -19,8 +19,9 @@ RareFactSharedCommand::RareFactSharedCommand(){
                string fileNameRoot;
                fileNameRoot = getRootName(globaldata->inputFileName);
                format = globaldata->getFormat();
+               convert(globaldata->getFreq(), freq);
+               convert(globaldata->getIters(), nIters);
                validCalculator = new ValidCalculators();
-               util = new SharedUtil();
                                
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
@@ -52,11 +53,9 @@ RareFactSharedCommand::RareFactSharedCommand(){
 //**********************************************************************************************************************
 
 RareFactSharedCommand::~RareFactSharedCommand(){
-       delete order;
        delete input;
        delete rCurve;
        delete read;
-       delete util;
 }
 
 //**********************************************************************************************************************
@@ -68,55 +67,81 @@ int RareFactSharedCommand::execute(){
                //if the users entered no valid calculators don't execute command
                if (rDisplays.size() == 0) { return 0; }
 
-               if (format == "sharedfile") {
-                       read = new ReadOTUFile(globaldata->inputFileName);      
-                       read->read(&*globaldata); 
+               read = new ReadOTUFile(globaldata->inputFileName);      
+               read->read(&*globaldata); 
                        
-                       input = globaldata->ginput;
-                       order = input->getSharedOrderVector();
-               }else {
-                       //you are using a list and a groupfile
-                       read = new ReadOTUFile(globaldata->inputFileName);      
-                       read->read(&*globaldata); 
+               input = globaldata->ginput;
+               lookup = input->getSharedRAbundVectors();
+               vector<SharedRAbundVector*> lastLookup = lookup;
                
-                       input = globaldata->ginput;
-                       SharedList = globaldata->gSharedList;
-                       order = SharedList->getSharedOrderVector();
+               if (lookup.size() < 2) { 
+                       cout << "I cannot run the command without at least 2 valid groups."; 
+                       for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+                       return 0;
                }
                
-               //set users groups
-               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "rarefact");
-               
-               while(order != NULL){
-               
-                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
-                               //create collectors curve
-                               rCurve = new Rarefact(order, rDisplays);
-                               convert(globaldata->getFreq(), freq);
-                               convert(globaldata->getIters(), nIters);
-                               rCurve->getSharedCurve(freq, nIters);
+               //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<int> userLines = globaldata->lines;
+       
+               //as long as you are not at the end of the file or done wih the lines you want
+               while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                        
+                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+                               
+                               rCurve = new Rarefact(lookup, rDisplays);
+                               rCurve->getSharedCurve(freq, nIters);
                                delete rCurve;
                        
-                               cout << order->getLabel() << '\t' << count << endl;
+                               cout << lookup[0]->getLabel() << '\t' << count << endl;
+                               processedLabels.insert(lookup[0]->getLabel());
+                               userLabels.erase(lookup[0]->getLabel());
+                               userLines.erase(count);
                        }
                        
-                       //get next line to process
-                       if (format == "sharedfile") {
-                               order = input->getSharedOrderVector();
-                       }else {
-                               //you are using a list and a groupfile
-                               SharedList = input->getSharedListVector(); //get new list vector to process
-                               if (SharedList != NULL) {
-                                       order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-                               }else {
-                                       break;
-                               }
+                       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);
+                                       rCurve->getSharedCurve(freq, nIters);
+                                       delete rCurve;
+
+                                       processedLabels.insert(lastLookup[0]->getLabel());
+                                       userLabels.erase(lastLookup[0]->getLabel());
                        }
+                               
+                       //prevent memory leak
+                       if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
+                       lastLookup = lookup;
                        
+                       //get next line to process
+                       lookup = input->getSharedRAbundVectors();
                        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(lastLookup[0]->getLabel()) != 1) {
+                               cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+                               needToRun = true;
+                       }else {
+                               cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+                       }
+               }
+               
+               //run last line if you need to
+               if (needToRun == true)  {
+                       cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+                       rCurve = new Rarefact(lastLookup, rDisplays);
+                       rCurve->getSharedCurve(freq, nIters);
+                       delete rCurve;
+               }
+               
+               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