X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=a404f79222ac83cf41d42c04ceb614df1e01dceb;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=cc175e17fd74f0d808fc9efa11442f582333e73d;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index cc175e1..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);
+			}
 		}
 		
 	}
@@ -282,10 +287,11 @@ int UnifracUnweightedCommand::execute() {
 		m->openOutputFile(sumFile, outSum);
 		
 		util = new SharedUtil();
-		vector<string> Groups = m->getGroups();
+		Groups = m->getGroups();
 		vector<string> namesGroups = tmap->getNamesOfGroups();
 		util->setGroups(Groups, namesGroups, allGroups, numGroups, "unweighted");	//sets the groups the user wants to analyze
 		util->getCombos(groupComb, Groups, numComp);
+		m->setGroups(Groups);
 		delete util;
 	
 		if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }