X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=nameassignment.cpp;h=1e42111e574baacf2eb2f5c3407416c9029f9041;hp=641be4e626fb9c52b9035a979acd95dbe654e35a;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=3102812d94898439646131cecdb64fc542913c87

diff --git a/nameassignment.cpp b/nameassignment.cpp
index 641be4e..1e42111 100644
--- 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();
 	
@@ -76,6 +77,7 @@ void NameAssignment::print(ostream& out){
 //cout << (*this).size() << endl;
 		for(it = (*this).begin(); it!=(*this).end(); it++){
 			out << it->first << '\t' <<  it->second << endl;  //prints out keys and values of the map this.
+			//out << it->first << '\t' <<  it->first << endl;
 		}
 	}
 	catch(exception& e) {