fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index ef1515863dbca8b0f930d1b26f3c9f2936c7eec4..afbacc00aaaec2b92c5d81278d16b463c0f43ffe 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -313,13 +313,7 @@ int ListSeqsCommand::readList(){
                                
                                if (m->control_pressed) { in.close(); return 0; }
                                
-                               while (binnames.find_first_of(',') != -1) { 
-                                       string name = binnames.substr(0,binnames.find_first_of(','));
-                                       binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
-                                       names.push_back(name);
-                               }
-                       
-                               names.push_back(binnames);
+                               m->splitAtComma(binnames, names);
                        }
                }
                in.close();     
@@ -349,14 +343,7 @@ int ListSeqsCommand::readName(){
                        in >> secondCol;                        
                        
                        //parse second column saving each name
-                       while (secondCol.find_first_of(',') != -1) { 
-                               name = secondCol.substr(0,secondCol.find_first_of(','));
-                               secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
-                               names.push_back(name);
-                       }
-                       
-                       //get name after last ,
-                       names.push_back(secondCol);
+                       m->splitAtComma(secondCol, names);
                        
                        m->gobble(in);
                }
@@ -413,14 +400,14 @@ int ListSeqsCommand::readAlign(){
                        if (!in.eof())  {       in >> junk;             }
                        else                    {       break;                  }
                }
-               
+               //m->getline(in);
                
                while(!in.eof()){
                
                        if (m->control_pressed) { in.close(); return 0; }
 
                        in >> name;                             //read from first column
-                       
+                       //m->getline(in);
                        //read rest
                        for (int i = 0; i < 15; i++) {  
                                if (!in.eof())  {       in >> junk;             }