pca command

[mothur.git] / getrelabundcommand.cpp

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 8c28c47b220e1554972d3cdb97bd2218af4f1c77..08e9228b215819f5e19e4d697137384294392422 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -275,8 +275,6 @@ int GetRelAbundCommand::execute(){
 
 int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
        try {
-               if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
-
                
                 for (int i = 0; i < thisLookUp.size(); i++) {
                        out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
@@ -320,48 +318,5 @@ int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp,
        }
 }
 //**********************************************************************************************************************
-int GetRelAbundCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
-       try {
-               
-               vector<SharedRAbundVector*> newLookup;
-               for (int i = 0; i < thislookup.size(); i++) {
-                       SharedRAbundVector* temp = new SharedRAbundVector();
-                       temp->setLabel(thislookup[i]->getLabel());
-                       temp->setGroup(thislookup[i]->getGroup());
-                       newLookup.push_back(temp);
-               }
-               
-               //for each bin
-               for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
-                       if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
-               
-                       //look at each sharedRabund and make sure they are not all zero
-                       bool allZero = true;
-                       for (int j = 0; j < thislookup.size(); j++) {
-                               if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
-                       }
-                       
-                       //if they are not all zero add this bin
-                       if (!allZero) {
-                               for (int j = 0; j < thislookup.size(); j++) {
-                                       newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
-                               }
-                       }
-               }
-
-               for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
-
-               thislookup = newLookup;
-               
-               return 0;
- 
-       }
-       catch(exception& e) {
-               m->errorOut(e, "GetRelAbundCommand", "eliminateZeroOTUS");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************