fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 4977cad1f769690e300013e89c936eefb4228e84..2117daff4f2558e26bcf0008666f87bee0180f4d 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -167,7 +167,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                        }
                        
                        namesfile = validParameter.validFile(parameters, "name", true);
-                       if (namesfile == "not open") { abort = true; }  
+                       if (namesfile == "not open") { namesfile = ""; abort = true; }  
                        else if (namesfile == "not found") { namesfile = ""; }
                        else {  m->setNameFile(namesfile); }
 
@@ -176,6 +176,11 @@ BinSeqCommand::BinSeqCommand(string option) {
                        else if (groupfile == "not found") { groupfile = ""; }
                        else { m->setGroupFile(groupfile); }
                        
+                       if (namesfile == ""){
+                               vector<string> files; files.push_back(fastafile); 
+                               parser.getNameFile(files);
+                       }
+                       
                }
        }
        catch(exception& e) {