X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=2d46efc9efebcfbe7807292cb814cf58686f9ac4;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=ccf29526f5e803049371c452bcdcf7ddad10da48;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index ccf2952..2d46efc 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -139,7 +139,7 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
 			if (randomtree == "")  {
 				//check for required parameters
 				treefile = validParameter.validFile(parameters, "tree", true);
-				if (treefile == "not open") { abort = true; }
+				if (treefile == "not open") { treefile = ""; abort = true; }
 				else if (treefile == "not found") { 				//if there is a current design file, use it
 					treefile = m->getTreeFile(); 
 					if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
@@ -153,7 +153,7 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
 				else { m->setGroupFile(groupfile); }
 				
 				namefile = validParameter.validFile(parameters, "name", true);
-				if (namefile == "not open") { abort = true; }
+				if (namefile == "not open") { namefile = ""; abort = true; }
 				else if (namefile == "not found") { namefile = ""; }
 				else { m->setNameFile(namefile); }
 			}
@@ -177,6 +177,11 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
 			m->setProcessors(temp);
 			m->mothurConvert(temp, processors);
 			
+			if (namefile == "") {
+				vector<string> files; files.push_back(treefile);
+				parser.getNameFile(files);
+			}
+			
 		}
 
 	}