fixed craig nelsons weighted bug and paralellized parsimony

[mothur.git] / helpcommand.h

diff --git a/helpcommand.h b/helpcommand.h
index d8f9b14d884e48d931f013f42badf8be4f38e42b..d4e7b1fda16a88f8e88a30a46ba70e50fe1ce290 100644 (file)
--- a/helpcommand.h
+++ b/helpcommand.h
@@ -12,19 +12,26 @@
 /* This class is designed to aid the user in running mothur. */
 
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "validcommands.h"
-
+#include "commandfactory.hpp"
 
 class HelpCommand : public Command {
        
 public:
-       HelpCommand();
+       HelpCommand(string);
+       HelpCommand() {}
        ~HelpCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
+       void help() {};
+       
 private:
-       GlobalData* globaldata;
-       ValidCommands* validCommands;
+       CommandFactory* validCommands;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       
        
 private: