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[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 403b2b86d9addf1f9291e7f87fac63ef1755c002..6e69cad4f8dbde50541a8daad71dbcce712b8953 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -144,16 +144,18 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                                        treefile = m->getTreeFile(); 
                                        if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
                                        else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }                                                               
-                               }       
+                               }else { m->setTreeFile(treefile); }     
                                
                                //check for required parameters
                                groupfile = validParameter.validFile(parameters, "group", true);
                                if (groupfile == "not open") { abort = true; }
                                else if (groupfile == "not found") { groupfile = ""; }
+                               else { m->setGroupFile(groupfile); }
                                
                                namefile = validParameter.validFile(parameters, "name", true);
                                if (namefile == "not open") { abort = true; }
                                else if (namefile == "not found") { namefile = ""; }
+                               else { m->setNameFile(namefile); }
                        }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter