changing command name classify.shared to classifyrf.shared

[mothur.git] / phylotypecommand.h

diff --git a/phylotypecommand.h b/phylotypecommand.h
index 30a578221f09042817534b51f91d8e33f3125c6c..ef8b8f17e37051be4951d6dd662d0db1beb1dbaa 100644 (file)
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -26,19 +26,22 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "phylotype";           }
        string getCommandCategory()             { return "Clustering";          }
-       string getHelpString(); 
        
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
+       string getDescription()         { return "cluster your sequences into OTUs based on their classifications"; }
+
        int execute();
        void help() { m->mothurOut(getHelpString()); }
        
 private:
        bool abort, allLines;
-       string taxonomyFileName, label, outputDir, namefile;
+       string taxonomyFileName, label, outputDir, namefile, countfile;
        set<string> labels; //holds labels to be used
        int cutoff;
        map<string, string> namemap;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        map<int, int> currentNodes;
        map<int, int> parentNodes;