changing command name classify.shared to classifyrf.shared

[mothur.git] / homovacommand.h

diff --git a/homovacommand.h b/homovacommand.h
index ec7a793bc25082fe12bf1fc768a72e0209d6b96a..22741e979ec9b0847ca660f5ab41eab49fe715d5 100644 (file)
--- a/homovacommand.h
+++ b/homovacommand.h
@@ -26,8 +26,12 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "homova";                                      }
        string getCommandCategory()             { return "Hypothesis Testing";          }
-       string getHelpString(); 
        
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. \nhttp://www.mothur.org/wiki/Homova"; }
+       string getDescription()         { return "homova"; }
+
        int execute();
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -38,7 +42,7 @@ 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;