X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setdircommand.h;h=36753edeb57f8601dd0a1f5309b9c1cf67109429;hp=565b839aadb6ce8f2f440e6bd8b75be44afba227;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=fbaa6c7ac44f857c1ece7c8199e9e7e09b4bbe74

diff --git a/setdircommand.h b/setdircommand.h
index 565b839..36753ed 100644
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -19,14 +19,27 @@ class SetDirectoryCommand : public Command {
 	
 public:
 	SetDirectoryCommand(string);
-	~SetDirectoryCommand();
-	int execute();
-	void help();
+	SetDirectoryCommand() { abort = true; calledHelp = true; setParameters(); }
+	~SetDirectoryCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "set.dir";		}
+	string getCommandCategory()		{ return "General";		}
+	
+	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;
+	
 		
 };