X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nameassignment.cpp;h=0c30898dd4085f5000a68c005ccbeee1bcd3650c;hb=813f0516e9c7533859f57ebe6d7b8854896bf009;hp=bc088f45924f4af9db951e81882376cd64fbc8f0;hpb=5f44783e6d74a9c207492ac244210c915cadc272;p=mothur.git

diff --git a/nameassignment.cpp b/nameassignment.cpp
index bc088f4..0c30898 100644
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -5,7 +5,7 @@
 //**********************************************************************************************************************
 
 NameAssignment::NameAssignment(string nameMapFile){
-	
+	m = MothurOut::getInstance();
 	openInputFile(nameMapFile, fileHandle);
 	
 }
@@ -17,26 +17,30 @@ void NameAssignment::readMap(){
 		string firstCol, secondCol, skip;
 	//	int index = 0;
 	
-	
-//		map<string, string> data;
+		
+		map<string, int>::iterator itData;
 		int rowIndex = 0;
-
+		
 		while(fileHandle){
 			fileHandle >> firstCol;				//read from first column
 			fileHandle >> secondCol;			//read from second column
+						
+			itData = (*this).find(firstCol);
+			if (itData == (*this).end()) {
+			
+				(*this)[firstCol] = rowIndex++;
+				list.push_back(secondCol);		//adds data's value to list
+				reverse[rowIndex] = firstCol;
+				
+			}else{	m->mothurOut(firstCol + " is already in namesfile. I will use first definition."); m->mothurOutEndLine();  }
 			
-//			data[firstCol] = secondCol;			//store data in map
-
-			list.push_back(secondCol);		//adds data's value to list
-			reverse[rowIndex] = firstCol;
-			(*this)[firstCol] = rowIndex++;
 			gobble(fileHandle);
 		}
 		fileHandle.close();
 	
 	}
 	catch(exception& e) {
-		errorOut(e, "NameAssignment", "readMap");
+		m->errorOut(e, "NameAssignment", "readMap");
 		exit(1);
 	}
 }
@@ -51,7 +55,7 @@ void NameAssignment::push_back(string name) {
 		list.push_back(name);
 	}
 	catch(exception& e) {
-		errorOut(e, "NameAssignment", "push_back");
+		m->errorOut(e, "NameAssignment", "push_back");
 		exit(1);
 	}
 }
@@ -75,7 +79,7 @@ void NameAssignment::print(ostream& out){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "NameAssignment", "print");
+		m->errorOut(e, "NameAssignment", "print");
 		exit(1);
 	}
 }