X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=a404f79222ac83cf41d42c04ceb614df1e01dceb;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=c09301f62be0cba7bb2eee024442cc94e6e5c0a3;hpb=4f2c7f477a1ef2d60a1c0c84ab1ba8243af67f87;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index c09301f..a404f79 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -155,7 +155,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(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); }
 			
@@ -171,7 +171,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 			}
 				
 			itersString = validParameter.validFile(parameters, "iters", false);				if (itersString == "not found") { itersString = "1000"; }
-			convert(itersString, iters); 
+			m->mothurConvert(itersString, iters); 
 			
 			string temp = validParameter.validFile(parameters, "distance", false);			
 			if (temp == "not found") { phylip = false; outputForm = ""; }
@@ -188,7 +188,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			if (!random) {  iters = 0;  } //turn off random calcs
 			
@@ -198,6 +198,11 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 				m->splitAtDash(groups, Groups);
 				m->setGroups(Groups);
 			}
+			
+			if (namefile == "") {
+				vector<string> files; files.push_back(treefile);
+				parser.getNameFile(files);
+			}
 		}
 		
 	}