X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=nameassignment.cpp;h=1e42111e574baacf2eb2f5c3407416c9029f9041;hp=cf4e6774c32706d506d472963bda6f9ac86df7f1;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=163b300cfd7d4ca4e70c454be20f07b1d8346650

diff --git a/nameassignment.cpp b/nameassignment.cpp
index cf4e677..1e42111 100644
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -5,47 +5,58 @@
 //**********************************************************************************************************************
 
 NameAssignment::NameAssignment(string nameMapFile){
-	
-	openInputFile(nameMapFile, fileHandle);
+	m = MothurOut::getInstance();
+	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
-			(*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();
 	
-//		map<string, string>::iterator it = data.begin();
-//		for(it;it!=data.end();it++){
-//			cout << it->first << endl;
-//			(*this)[it->first] = rowIndex;
-//			rowIndex++;
-//		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the NameAssignment class Function readMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "NameAssignment", "readMap");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the NameAssignment class function readMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+void NameAssignment::push_back(string name) {
+	try{
+	
+		int num = (*this).size();
+		(*this)[name] = num;
+		reverse[num] = name;
+		
+		list.push_back(name);
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NameAssignment", "push_back");
 		exit(1);
 	}
 }
@@ -60,19 +71,17 @@ ListVector NameAssignment::getListVector(void){
 
 //**********************************************************************************************************************
 
-void NameAssignment::print(void){
+void NameAssignment::print(ostream& out){
 	try {
-		map<string,int>::iterator it = (*this).begin();
-		for(it;it!=(*this).end();it++){
-			cout << it->first << '\t' << it->second << endl;  //prints out keys and values of the map this.
+		map<string,int>::iterator it;
+//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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the NameAssignment class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the NameAssignment class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "NameAssignment", "print");
 		exit(1);
 	}
 }
@@ -80,10 +89,35 @@ void NameAssignment::print(void){
 //**********************************************************************************************************************
 
 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 {
+	
+		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);
+	}
+}
 //**********************************************************************************************************************