added cutoff change to mgcluster

[mothur.git] / nmdscommand.cpp

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 3f8e34249c3d15c94709262fd252db1b525c820a..946aa68ab24ed5a10800d6d5c9e2ca32f4fd2ade 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -77,6 +77,7 @@ NMDSCommand::NMDSCommand(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();
@@ -127,7 +128,7 @@ NMDSCommand::NMDSCommand(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); } 
                        
                        axesfile = validParameter.validFile(parameters, "axes", true);
                        if (axesfile == "not open") { axesfile = ""; abort = true; }