Changed back to xcode build.

[mothur.git] / normalizesharedcommand.cpp

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 93bc7f29a075126c9cb70bcc6f2590bd222a574d..16b9732ebdb25e936bbda1537825467f400cf079 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -12,7 +12,7 @@
 //**********************************************************************************************************************
 vector<string> NormalizeSharedCommand::getValidParameters(){   
        try {
-               string Array[] =  {"groups","label","scale","outputdir","inputdir","norm"};
+               string Array[] =  {"groups","label","method","outputdir","inputdir","norm"};
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                return myArray;
        }
@@ -71,7 +71,7 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) {
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {"groups","label","scale","outputdir","inputdir","norm"};
+                       string AlignArray[] =  {"groups","label","method","outputdir","inputdir","norm"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -310,7 +310,8 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, o
                                        float newNorm = relabund * norm;
                                        //round to nearest int
                                        finalNorm = (int) floor((newNorm + 0.5));
-                                       
+                                       //cout << thisLookUp[i]->getGroup() << '\t' << abund << '\t' << relabund << '\t' << norm << '\t' << newNorm << '\t' << finalNorm << endl;
+                               
                                }else{ m->mothurOut(method + " is not a valid scaling option."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
                                
                                //cout << finalNorm << '\t';
@@ -322,7 +323,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, o
                 eliminateZeroOTUS(thisLookUp);
                 
                  for (int i = 0; i < thisLookUp.size(); i++) {
-                       out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
+                       out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t';
                        thisLookUp[i]->print(out);
                 }