working on pam

[mothur.git] / hclustercommand.h

diff --git a/hclustercommand.h b/hclustercommand.h
index 5fbdb3d1ab3bfe15a141c1d710ea6d84186a07db..1b8e9b7607df66c0a36621f31ced21772f36a909 100644 (file)
--- a/hclustercommand.h
+++ b/hclustercommand.h
@@ -18,7 +18,7 @@
 #include "readcluster.h"
 
 /******************************************************************/
-//This command is an implementation of the HCluster algorythmn described in 
+//This command is an implementation of the HCluster algorithmn described in 
 //ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences by
 //Yijun Sun1,2,*, Yunpeng Cai2, Li Liu1, Fahong Yu1, Michael L. Farrell3, William McKendree3 
 //and William Farmerie1 1 
@@ -36,10 +36,14 @@ public:
        ~HClusterCommand(){}
        
        vector<string> setParameters();
-       string getCommandName()                 { return "hcluster";                            }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getHelpString(); 
+       string getCommandName()                 { return "hcluster";    }
+       string getCommandCategory()             { return "Clustering";  }
        
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Sun Y, Cai Y, Liu L, Yu F, Farrell ML, Mckendree W, Farmerie W (2009). ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76. \nhttp://www.mothur.org/wiki/Hcluster"; }
+       string getDescription()         { return "cluster your sequences into OTUs using a distance matrix"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }