X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=otuhierarchycommand.cpp;h=07e3c1d0146ef521563697fe07deb38d7837b67d;hp=dc026decc9db9916513fcbd1d41fe23298173717;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index dc026de..07e3c1d 100644
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -175,23 +175,15 @@ int OtuHierarchyCommand::execute(){
 		}
 		
 		//map sequences to bin number in the "little" otu
-		map<string, int> littleBins; 
+		map<string, int> littleBins;
+        vector<string> binLabels0 = lists[0].getLabels();
 		for (int i = 0; i < lists[0].getNumBins(); i++) {
 		
 			if (m->control_pressed) {  return 0; }
-			
-			string names = lists[0].get(i); 
-			
-			//parse bin
-			while (names.find_first_of(',') != -1) { 
-				string name = names.substr(0,names.find_first_of(','));
-				names = names.substr(names.find_first_of(',')+1, names.length());
-				littleBins[name] = i;  
-			}
-			
-			//get last name
-			littleBins[names] = i;
-		}
+			string bin = lists[0].get(i);
+            vector<string> names; m->splitAtComma(bin, names);
+			for (int j = 0; j < names.size(); j++) { littleBins[names[j]] = i; }
+        }
 		
 		ofstream out;
         map<string, string> variables; 
@@ -203,33 +195,28 @@ int OtuHierarchyCommand::execute(){
 		m->openOutputFile(outputFileName, out);
 		
 		//go through each bin in "big" otu and output the bins in "little" otu which created it
+        vector<string> binLabels1 = lists[1].getLabels();
 		for (int i = 0; i < lists[1].getNumBins(); i++) {
 		
 			if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
 			
-			string names = lists[1].get(i);
+			string binnames = lists[1].get(i);
+            vector<string> names; m->splitAtComma(binnames, names);
 			
 			//output column 1
-			if (output == "name")	{   out << names << '\t';	}
-			else					{	out << i << '\t';		}
+			if (output == "name")	{   out << binnames << '\t';	}
+			else					{	out << binLabels1[i] << '\t';		}
 			
 			map<int, int> bins; //bin numbers in little that are in this bin in big
 			map<int, int>::iterator it;
 			
 			//parse bin
-			while (names.find_first_of(',') != -1) { 
-				string name = names.substr(0,names.find_first_of(','));
-				names = names.substr(names.find_first_of(',')+1, names.length());
-				bins[littleBins[name]] = littleBins[name];  
-			}
-			
-			//get last name
-			bins[littleBins[names]] = littleBins[names]; 
+			for (int j = 0; j < names.size(); j++) { bins[littleBins[names[j]]] = littleBins[names[j]];   }
 			
 			string col2 = "";
 			for (it = bins.begin(); it != bins.end(); it++) {
 				if (output == "name")	{   col2 += lists[0].get(it->first) + "\t";	}
-				else					{	col2 += toString(it->first) + "\t";		}
+				else					{	col2 += binLabels0[it->first] + "\t";		}
 			}
 			
 			//output column 2