added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / nameassignment.cpp

diff --git a/nameassignment.cpp b/nameassignment.cpp
index 0a62a032077fd58c5ee92c3801662a9e280f6df7..126c4e0c594b6745ec6a7c4fcd5228c717d67677 100644 (file)
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -6,7 +6,7 @@
 
 NameAssignment::NameAssignment(string nameMapFile){
        m = MothurOut::getInstance();
-       openInputFile(nameMapFile, fileHandle);
+       m->openInputFile(nameMapFile, fileHandle);
        
 }
 
@@ -22,7 +22,7 @@ void NameAssignment::readMap(){
                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 +34,7 @@ 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();