working on pam

[mothur.git] / cooccurrencecommand.h

diff --git a/cooccurrencecommand.h b/cooccurrencecommand.h
index 8f60e08330ced9099c8b3b777e618a94ca2f9ed1..94930ac2db71fff68a9fb208385a6cdc2c94ade4 100644 (file)
--- a/cooccurrencecommand.h
+++ b/cooccurrencecommand.h
@@ -26,10 +26,12 @@ public:
        ~CooccurrenceCommand(){}
        
        vector<string> setParameters();
-       string getCommandName()                 { return "Cooccurrence";                        }
+       string getCommandName()                 { return "cooccurrence";                        }
        string getCommandCategory()             { return "Hypothesis Testing";  }
+       
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Cooccurrence"; }
+    string getOutputPattern(string);   
+       string getCitation() { return "Ulrich W & Gotelli NJ (2010).  Null model analysis of species associations using abundance data.  Ecology  91:3384.\nhttp://www.mothur.org/wiki/Cooccurrence"; }
        string getDescription()         { return "calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance."; }
        
        int execute();