changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / createdatabasecommand.cpp

diff --git a/createdatabasecommand.cpp b/createdatabasecommand.cpp
index 1da67e6d8694096da74ce8f855b27cf3b96d2f89..57d5264b8b151d4175b6754ab2ee75732e1e597e 100644 (file)
--- 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 {