changed added group output to indicator command. a few changes to work with the guy

[mothur.git] / amovacommand.h

diff --git a/amovacommand.h b/amovacommand.h
index f50df46f70a3c6cce602ba8eeb5a4987c6dd2c95..17dbae650912c5f4c21e0c8924dce3a676cc4fda 100644 (file)
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -23,7 +23,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "amova";                                       }
        string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
+       string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
+       string getDescription()         { return "analysis of molecular variance"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }
@@ -35,7 +38,7 @@ private:
        map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
 
        bool abort;
-       vector<string> outputNames;
+       vector<string> outputNames, Sets;
 
        string outputDir, inputDir, designFileName, phylipFileName;
        GroupMap* designMap;