sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / setdircommand.h

diff --git a/setdircommand.h b/setdircommand.h
index 0d12e05be43ce8ec055fa5a9bdc39dad62f9bca2..ab174c2b783eca5c3a7fc0d74a8a2f6c5abf4a70 100644 (file)
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -25,15 +25,19 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "set.dir";             }
        string getCommandCategory()             { return "General";             }
-       string getHelpString(); 
        
+       string getHelpString(); 
+    string getOutputPattern(string){ return ""; }      
+       string getCitation() { return "http://www.mothur.org/wiki/Set.dir"; }
+       string getDescription()         { return "set input, output and default directories"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
        CommandFactory* commandFactory;
        string output, input, tempdefault;
-       bool abort;
+       bool abort, debugOnly;
        vector<string> outputNames;