working on current change

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index c03fcc1ac133572fc7d821816edadc0b1fc32ecb..ef23375df9425f11816acbf8594f46e613e9e148 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -129,11 +129,12 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                        abort = true; 
                                }
                        }else if (taxonomyFileName == "not open") { abort = true; }     
+                       else { m->setTaxonomyFile(taxonomyFileName); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
-                       else { readNamesFile(); }       
+                       else { readNamesFile(); m->setNameFile(namefile); }     
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){