X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.cpp;fp=amovacommand.cpp;h=74fbda7ff6164128551bead9cfb4c8bfabb7ba0e;hb=f6c7165727bc17a5fbbcbb774d75ccffeb7f3da5;hp=b9b5deeb5e670ef2f119eb09bded37ab870efe4d;hpb=85bf2e965f12d609c751763883b2224e6951eeba;p=mothur.git

diff --git a/amovacommand.cpp b/amovacommand.cpp
index b9b5dee..74fbda7 100644
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -115,12 +115,12 @@ AmovaCommand::AmovaCommand(string option) {
 			
 			phylipFileName = validParameter.validFile(parameters, "phylip", true);
 			if (phylipFileName == "not open") { phylipFileName = ""; abort = true; }
-			else if (phylipFileName == "not found") { phylipFileName = ""; }	
-			else if (designFileName == "not found") {
-				designFileName = "";
-				m->mothurOut("You must provide an phylip file.");
-				m->mothurOutEndLine();
-				abort = true;
+			else if (phylipFileName == "not found") { 
+				phylipFileName = ""; 
+				
+				//check currentFiles for a phylip file
+				if (currentFiles->getPhylipFile() != "") {  phylipFileName = currentFiles->getPhylipFile(); m->mothurOut("Using " + phylipFileName + " as phylip file."); m->mothurOutEndLine();
+				}else { m->mothurOut("You must provide an phylip file."); m->mothurOutEndLine(); abort = true;  }
 			}	
 			
 			//check for required parameters
@@ -128,9 +128,10 @@ AmovaCommand::AmovaCommand(string option) {
 			if (designFileName == "not open") { abort = true; }
 			else if (designFileName == "not found") {
 				designFileName = "";
-				m->mothurOut("You must provide an design file.");
-				m->mothurOutEndLine();
-				abort = true;
+				
+				//check currentFiles for a design file
+				if (currentFiles->getDesignFile() != "") {  designFileName = currentFiles->getPhylipFile(); m->mothurOut("Using " + designFileName + " as phylip file."); m->mothurOutEndLine();
+				}else { m->mothurOut("You must provide an design file."); m->mothurOutEndLine(); abort = true;  }
 			}	
 
 			string temp = validParameter.validFile(parameters, "iters", false);