classify.seqs allows sequences to be in taxonomy file that are not in template. ...

[mothur.git] / cooccurrencecommand.h

diff --git a/cooccurrencecommand.h b/cooccurrencecommand.h
index da7cde84a5372acb083e509b0fb0a997039ad835..08209190f3f51b0e334706530afed253684eb75e 100644 (file)
--- a/cooccurrencecommand.h
+++ b/cooccurrencecommand.h
@@ -28,9 +28,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "Cooccurrence";                        }
        string getCommandCategory()             { return "Hypothesis Testing";  }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Cooccurrence"; }
-       string getDescription()         { return "Cooccurrence"; }
+       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(); 
        void help() { m->mothurOut(getHelpString()); }