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

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 717b1d3231c20368a2d23e9b86d52a6707f03b12..aebba6bbc430a6608d5fe8bb0a31ef9ebd58c4f4 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -639,34 +639,13 @@ int SubSampleCommand::getNames() {
 int SubSampleCommand::readNames() {
        try {
                
-               ifstream in;
-               m->openInputFile(namefile, in);
-               
-               string thisname, repnames;
-               map<string, vector<string> >::iterator it;
-               
-               while(!in.eof()){
-                       
-                       if (m->control_pressed) { in.close(); return 0; }
-                       
-                       in >> thisname;         m->gobble(in);          //read from first column
-                       in >> repnames;                 //read from second column
-                       
-                       it = nameMap.find(thisname);
-                       if (it == nameMap.end()) {
-                               
-                               vector<string> splitRepNames;
-                               m->splitAtComma(repnames, splitRepNames);
-                               
-                               nameMap[thisname] = splitRepNames;      
-                               for (int i = 0; i < splitRepNames.size(); i++) { names.push_back(splitRepNames[i]); }
-                               
-                       }else{  m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine();  }
-                       
-                       m->gobble(in);
-               }
-               in.close();     
-               
+        nameMap.clear();
+        m->readNames(namefile, nameMap);
+        
+        //save names of all sequences
+        map<string, vector<string> >::iterator it;
+        for (it = nameMap.begin(); it != nameMap.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { names.push_back((it->second)[i]); } }
+        
                return 0;
                
        }