adding labels to list file.

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index dc026decc9db9916513fcbd1d41fe23298173717..07e3c1d0146ef521563697fe07deb38d7837b67d 100644 (file)
--- 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