X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=normalizesharedcommand.cpp;h=16b9732ebdb25e936bbda1537825467f400cf079;hb=cdf9083dc32543cc640e72e9ca3aee0323cbad45;hp=93bc7f29a075126c9cb70bcc6f2590bd222a574d;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 93bc7f2..16b9732 100644
--- 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);
 		 }