X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.cpp;fp=pcoacommand.cpp;h=20e8e1be712765513c1f581b4e94536207f4f773;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=5d917372e5f88a5a45b762efc57ab388d80a4ebc;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 5d91737..20e8e1b 100644
--- 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;