X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setdircommand.h;h=36753edeb57f8601dd0a1f5309b9c1cf67109429;hp=0d12e05be43ce8ec055fa5a9bdc39dad62f9bca2;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/setdircommand.h b/setdircommand.h
index 0d12e05..36753ed 100644
--- 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, modifyNames;
 	vector<string> outputNames;