X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=createdatabasecommand.cpp;h=57d5264b8b151d4175b6754ab2ee75732e1e597e;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=1da67e6d8694096da74ce8f855b27cf3b96d2f89;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/createdatabasecommand.cpp b/createdatabasecommand.cpp
index 1da67e6..57d5264 100644
--- a/createdatabasecommand.cpp
+++ b/createdatabasecommand.cpp
@@ -209,7 +209,7 @@ int CreateDatabaseCommand::execute(){
         
         //names redundants to uniques. backwards to how we normally do it, but each bin is the list file will be a key entry in the map.
         map<string, string> repNames;
-        int numUniqueNamesFile = readNames(repNames);
+        int numUniqueNamesFile = m->readNames(repnamesfile, repNames);
         
         //are there the same number of otus in the fasta and name files
         if (repOtusSizes.size() != numUniqueNamesFile) { m->mothurOut("[ERROR]: you have " + toString(numUniqueNamesFile) + " unique seqs in your repname file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file.  These should match.\n"); m->control_pressed = true; }
@@ -394,32 +394,6 @@ vector<int> CreateDatabaseCommand::readFasta(vector<Sequence>& seqs){
 		exit(1);
 	}
 }
-/**********************************************************************************************************************/
-int CreateDatabaseCommand::readNames(map<string, string>& nameMap) { 
-	try {
-		
-		//open input file
-		ifstream in;
-		m->openInputFile(repnamesfile, in);
-		
-		while (!in.eof()) {
-			if (m->control_pressed) { break; }
-			
-			string firstCol, secondCol;
-			in >> firstCol >> secondCol; m->gobble(in);
-			
-			nameMap[secondCol] = firstCol;
-		}
-		in.close();
-		
-		return nameMap.size();
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "CreateDatabaseCommand", "readNames");
-		exit(1);
-	}
-}
 //**********************************************************************************************************************
 ListVector* CreateDatabaseCommand::getList(){
 	try {