working on current change

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 5d917372e5f88a5a45b762efc57ab388d80a4ebc..20e8e1be712765513c1f581b4e94536207f4f773 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -111,7 +111,7 @@ PCOACommand::PCOACommand(string option)  {
                                phylipfile = m->getPhylipFile(); 
                                if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setPhylipFile(phylipfile); } 
                        
                        filename = phylipfile;