fixed bug with get.oturep and fixed problem with errorcheckor that did not allow...

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 064455f49e28538c95858ba574dc9ef3b0cc9289..6daad979d741f56290ac7e40979de956a705e1ee 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -20,11 +20,19 @@ GetOTURepCommand::GetOTURepCommand(){
                if(globaldata->gListVector != NULL)             {       
                        listOfNames = new ListVector(*globaldata->gListVector); 
                        
+                       vector<string> names;
+                       string binnames;
                        //map names to rows in sparsematrix
                        for (int i = 0; i < listOfNames->size(); i++) {
-                               nameToIndex[listOfNames->get(i)] = i;
+                               names.clear();
+                               binnames = listOfNames->get(i);
+                               splitAtComma(binnames, names);
+                               
+                               for (int j = 0; j < names.size(); j++) {
+                                       nameToIndex[names[j]] = i;
+                               }
                        }
-               }else { cout << "error" << endl; }
+               }else { cout << "error, no listvector." << endl; }
 
                
                fastafile = globaldata->getFastaFile();
@@ -176,7 +184,7 @@ string GetOTURepCommand::FindRep(int bin) {
                string minName;
                
                binnames = list->get(bin);
-               
+       
                //parse names into vector
                splitAtComma(binnames, names);
                
@@ -186,6 +194,7 @@ string GetOTURepCommand::FindRep(int bin) {
                        //fill binMap
                        for (int i = 0; i < names.size(); i++) {
                                for (it3 = nameToIndex.begin(); it3 != nameToIndex.end(); it3++) {
+
                                        if (it3->first == names[i]) {  
                                                binMap[it3->second] = it3->first;