paralellized the indicator command

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 607256bc108d33f1b1b869bd3250c49900f385c6..20e8e1be712765513c1f581b4e94536207f4f773 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -69,6 +69,7 @@ PCOACommand::PCOACommand(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();
@@ -110,7 +111,7 @@ PCOACommand::PCOACommand(string option)  {
                                phylipfile = m->getPhylipFile(); 
                                if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setPhylipFile(phylipfile); } 
                        
                        filename = phylipfile;