removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / setdircommand.h

diff --git a/setdircommand.h b/setdircommand.h
index 6263c5eb9a55c391a0a91adf657b82d2be97d6cf..0d12e05be43ce8ec055fa5a9bdc39dad62f9bca2 100644 (file)
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "commandfactory.hpp"
-#include "globaldata.hpp"
 
 /**********************************************************/
 
@@ -20,21 +19,23 @@ 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(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        CommandFactory* commandFactory;
        string output, input, tempdefault;
        bool abort;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
+       
                
 };