added amova command

diff --git a/amovacommand.cpp b/amovacommand.cpp
index a88baf0a673d9e3c8cd34313962d808448ce7f54..d46cf740bd744697cc5caccdd2724d31edca6bac 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -173,7 +173,7 @@ AmovaCommand::AmovaCommand(string option) {
                                        m->mothurOut("You must read a list and a group, a shared file or provide a distance matrix before you can use the amova command."); m->mothurOutEndLine(); abort = true; 
                                }
                        }else { sharedfile = globaldata->getSharedFile(); } 
-                       
+                               
                        //use distance matrix if one is provided
                        if ((sharedfile != "") && (phylipfile != "")) { sharedfile = ""; }
                        
@@ -412,7 +412,7 @@ int AmovaCommand::execute(){
                                out.close();
                        }
                        
-                       InputData input("sharedfile", sharedfile);
+                       InputData input(sharedfile, "sharedfile");
                        vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
                        string lastLabel = lookup[0]->getLabel();