nmds command done

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 4adb57c6147c544ab9284996d85a8bf4db9e55e2..0661f24b09d4494d658a6044fdce1fafe0b5582f 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -127,7 +127,7 @@ NMDSCommand::NMDSCommand(string option)  {
                                outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it      
                        }
                        
-                       string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "1";     }
+                       string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "2";     }
                        convert(temp, mindim);
                        
                        temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
@@ -160,7 +160,7 @@ void NMDSCommand::help(){
                m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
                m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine();
                m->mothurOut("The maxdim parameter allows you to select how maximum dimensions to use. Default=2"); m->mothurOutEndLine();
-               m->mothurOut("The mindim parameter allows you to select how minimum dimensions to use. Default=1"); m->mothurOutEndLine();
+               m->mothurOut("The mindim parameter allows you to select how minimum dimensions to use. Default=2"); m->mothurOutEndLine();
                m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500"); m->mothurOutEndLine();
                m->mothurOut("The iters parameter allows you to select the number of random configuration to try. Default=10"); m->mothurOutEndLine();
                m->mothurOut("The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12."); m->mothurOutEndLine();