indicator command

[mothur.git] / nmdscommand.cpp

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 8fa0145ea7e97081000ee99337309861a0f8c7a9..946aa68ab24ed5a10800d6d5c9e2ca32f4fd2ade 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -46,7 +46,7 @@ string NMDSCommand::getHelpString(){
                helpString += "The iters parameter allows you to select the number of random configuration to try. Default=10\n"; 
                helpString += "The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12.\n"; 
                helpString += "Example nmds(phylip=yourDistanceFile).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -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; }