Merge remote-tracking branch 'origin/master'

[mothur.git] / setdircommand.h

diff --git a/setdircommand.h b/setdircommand.h
index 330adf14ee11061c9b049b6aab2bde783113d6d0..837a8b58053cc7b2f5491d8fb59ba00c7c758328 100644 (file)
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "commandfactory.hpp"
-#include "globaldata.hpp"
 
 /**********************************************************/
 
@@ -20,14 +19,26 @@ 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 getOutputFileNameTag(string, string) { return ""; }
+       string getHelpString(); 
+       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;
+       
                
 };