fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index b007db1f6eddc2d8e6119add616803b1d58526a2..f9dc450444b242555710f91dc3567f96e69e6d3d 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -141,7 +141,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        
                        //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(); }
@@ -155,7 +155,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(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); }
                        
@@ -192,6 +192,11 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        m->mothurConvert(temp, processors);
                        
                        if (!random) {  iters = 0;  } //turn off random calcs
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(treefile);
+                               parser.getNameFile(files);
+                       }
                }