fixes while testing 1.33.0

[mothur.git] / nameassignment.cpp

diff --git a/nameassignment.cpp b/nameassignment.cpp
index 0a62a032077fd58c5ee92c3801662a9e280f6df7..1e42111e574baacf2eb2f5c3407416c9029f9041 100644 (file)
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -6,23 +6,24 @@
 
 NameAssignment::NameAssignment(string nameMapFile){
        m = MothurOut::getInstance();
-       openInputFile(nameMapFile, fileHandle);
+       m->openInputFile(nameMapFile, fileHandle);
        
 }
-
+//**********************************************************************************************************************
+NameAssignment::NameAssignment(){ m = MothurOut::getInstance(); }
 //**********************************************************************************************************************
 
 void NameAssignment::readMap(){
        try{
                string firstCol, secondCol, skip;
        //      int index = 0;
-       
+        
                
                map<string, int>::iterator itData;
                int rowIndex = 0;
                
                while(fileHandle){
-                       fileHandle >> firstCol;                         //read from first column
+                       fileHandle >> firstCol; m->gobble(fileHandle);                  //read from first column
                        fileHandle >> secondCol;                        //read from second column
                                                
                        itData = (*this).find(firstCol);
@@ -34,7 +35,7 @@ void NameAssignment::readMap(){
                                
                        }else{  m->mothurOut(firstCol + " is already in namesfile. I will use first definition."); m->mothurOutEndLine();  }
                        
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                }
                fileHandle.close();