From: westcott <westcott>
Date: Wed, 8 Dec 2010 16:52:46 +0000 (+0000)
Subject: get.oturep ifstream
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=64b2b8d59acac0332e61b6622e7d16a300bdce3e

get.oturep ifstream
---

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 44c58c3..9cc9973 100644
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -560,14 +560,15 @@ int GetOTURepCommand::execute(){
 //**********************************************************************************************************************
 void GetOTURepCommand::readNamesFile() {
 	try {
+		ifstream in;
 		vector<string> dupNames;
-		m->openInputFile(namefile, inNames);
+		m->openInputFile(namefile, in);
 		
 		string name, names, sequence;
 	
-		while(!inNames.eof()){
-			inNames >> name;			//read from first column  A
-			inNames >> names;		//read from second column  A,B,C,D
+		while(!in.eof()){
+			in >> name;			//read from first column  A
+			in >> names;		//read from second column  A,B,C,D
 			
 			dupNames.clear();
 			
@@ -580,9 +581,9 @@ void GetOTURepCommand::readNamesFile() {
 				fasta->push_back(dupNames[i], sequence);
 			}
 		
-			m->gobble(inNames);
+			m->gobble(in);
 		}
-		inNames.close();
+		in.close();
 
 	}
 	catch(exception& e) {
@@ -594,14 +595,15 @@ void GetOTURepCommand::readNamesFile() {
 //read names file to find the weighted rep for each bin
 void GetOTURepCommand::readNamesFile(bool w) {
 	try {
+		ifstream in;
 		vector<string> dupNames;
-		m->openInputFile(namefile, inNames);
+		m->openInputFile(namefile, in);
 		
 		string name, names, sequence;
 		
-		while(!inNames.eof()){
-			inNames >> name;	m->gobble(inNames);		//read from first column  A
-			inNames >> names;							//read from second column  A,B,C,D
+		while(!in.eof()){
+			in >> name;	m->gobble(in);		//read from first column  A
+			in >> names;							//read from second column  A,B,C,D
 			
 			dupNames.clear();
 			
@@ -612,9 +614,9 @@ void GetOTURepCommand::readNamesFile(bool w) {
 				nameFileMap[dupNames[i]] = name;
 			}
 			
-			m->gobble(inNames);
+			m->gobble(in);
 		}
-		inNames.close();
+		in.close();
 		
 	}
 	catch(exception& e) {
diff --git a/mothur b/mothur
index a3b2f0f..0f23015 100755
Binary files a/mothur and b/mothur differ