paralellized the indicator command

[mothur.git] / clusterdoturcommand.cpp

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 2b7b02b63a3a97d683d16a01b4514c5aa2671626..3f629dc09af39d7c9785a18687d9aecb8bee5f58 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -72,6 +72,7 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -131,13 +132,14 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                                        m->mothurOut("You need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine(); 
                                        abort = true; 
                                }       
-                       }       
+                       }else { m->setPhylipFile(phylipfile); } 
 
                
                        //check for optional parameter and set defaults
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);