working on current change

[mothur.git] / deuniquetreecommand.cpp

diff --git a/deuniquetreecommand.cpp b/deuniquetreecommand.cpp
index 7f33ad65e13a44ed77dc2fab585cbded550475ad..f39a182ed863893c66f9b22a25c4c6765c04d165 100644 (file)
--- a/deuniquetreecommand.cpp
+++ b/deuniquetreecommand.cpp
@@ -116,7 +116,7 @@ DeuniqueTreeCommand::DeuniqueTreeCommand(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); }     
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
@@ -124,7 +124,7 @@ DeuniqueTreeCommand::DeuniqueTreeCommand(string option)  {
                                namefile = m->getNameFile(); 
                                if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current name file and the name parameter is required."); m->mothurOutEndLine(); abort = true; }                                                               
-                       }
+                       }else { m->setNameFile(namefile); }
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(treefile);       }
                }