1.23.0

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index a0d710e7b2ebbb7cffaf4aca88365a3ab73a197c..b007db1f6eddc2d8e6119add616803b1d58526a2 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -172,7 +172,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(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 = ""; }
@@ -189,7 +189,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(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
                }
@@ -277,10 +277,11 @@ int UnifracWeightedCommand::execute() {
                        
                util = new SharedUtil();
                string s; //to make work with setgroups
-               vector<string> Groups = m->getGroups();
+               Groups = m->getGroups();
                vector<string> nameGroups = tmap->getNamesOfGroups();
                util->setGroups(Groups, nameGroups, s, numGroups, "weighted");  //sets the groups the user wants to analyze
                util->getCombos(groupComb, Groups, numComp);
+               m->setGroups(Groups);
                delete util;
                
                weighted = new Weighted(tmap, includeRoot);