X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.cpp;fp=amovacommand.cpp;h=141673375fb8bb1a37e67980df9708fe6d2da126;hb=220dc345e493cddc569521111ce32ac4d965ab7f;hp=ad5823b15e108396ee1b0e0977167c8e4f1fbb22;hpb=23e60689fa4306234b3d05b116f25d198316d1ae;p=mothur.git

diff --git a/amovacommand.cpp b/amovacommand.cpp
index ad5823b..1416733 100644
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -122,17 +122,17 @@ AmovaCommand::AmovaCommand(string option) {
 				phylipFileName = m->getPhylipFile(); 
 				if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " 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(phylipFileName); }
 			
 			//check for required parameters
 			designFileName = validParameter.validFile(parameters, "design", true);
-			if (designFileName == "not open") { abort = true; }
+			if (designFileName == "not open") { designFileName = ""; abort = true; }
 			else if (designFileName == "not found") {
 				//if there is a current design file, use it
 				designFileName = m->getDesignFile(); 
 				if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }				
-			}	
+			}else { m->setDesignFile(designFileName); }	
 
 			string temp = validParameter.validFile(parameters, "iters", false);
 			if (temp == "not found") { temp = "1000"; }