fixes while testing 1.33.0

[mothur.git] / setdircommand.h

diff --git a/setdircommand.h b/setdircommand.h
index 6263c5eb9a55c391a0a91adf657b82d2be97d6cf..36753edeb57f8601dd0a1f5309b9c1cf67109429 100644 (file)
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "commandfactory.hpp"
-#include "globaldata.hpp"
 
 /**********************************************************/
 
@@ -20,21 +19,27 @@ class SetDirectoryCommand : public Command {
        
 public:
        SetDirectoryCommand(string);
-       SetDirectoryCommand() { abort = true; calledHelp = true; }
-       ~SetDirectoryCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       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;
-       map<string, vector<string> > outputTypes;
+       
                
 };