X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=nameassignment.cpp;h=1e42111e574baacf2eb2f5c3407416c9029f9041;hp=42d374d0b9e74842e4d3f289c75ae61645556ebd;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0

diff --git a/nameassignment.cpp b/nameassignment.cpp
index 42d374d..1e42111 100644
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -6,31 +6,36 @@
 
 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, string> data;
+        
+		
+		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);
+			if (itData == (*this).end()) {
 			
-//			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);
+				(*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();  }
+			
+			m->gobble(fileHandle);
 		}
 		fileHandle.close();
 	
@@ -72,6 +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) {
@@ -83,16 +89,35 @@ void NameAssignment::print(ostream& out){
 //**********************************************************************************************************************
 
 int NameAssignment::get(string key){
-	
-	return	(*this)[key];	
-
+	try {
+		map<string, int>::iterator itGet = (*this).find(key);
+		
+		//if you can't find it
+		if (itGet == (*this).end()) { return -1; }
+		
+		return	(*this)[key];	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NameAssignment", "get");
+		exit(1);
+	}
 }
 //**********************************************************************************************************************
 
 string NameAssignment::get(int key){
+	try {
 	
-	return	reverse[key];	
-
+		map<int, string>::iterator itGet = reverse.find(key);
+	
+		if (itGet == reverse.end()) { return "not found"; }
+	
+		return	reverse[key];	
+	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NameAssignment", "get");
+		exit(1);
+	}
 }
 //**********************************************************************************************************************