added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / command.hpp

diff --git a/command.hpp b/command.hpp
index 1dd5e871aaa66362e02e997c9ff26b427ed9178a..22f118164eb04e7d22c0438e3e42c56b79ed0f3d 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -1,6 +1,6 @@
 #ifndef COMMAND_HPP
 #define COMMAND_HPP
-
+//test2
 /*
  *  command.h
  *  
@@ -16,13 +16,39 @@
 #include "mothur.h"
 #include "optionparser.h"
 #include "validparameter.h"
+#include "mothurout.h"
+#include "commandparameter.h"
+
 
 class Command {
        
        public:
+               Command() {  m = MothurOut::getInstance();   } 
+               
+               //needed by gui
+               virtual string getCommandName() = 0;
+               virtual string getCommandCategory() = 0;
+               virtual string getHelpString() = 0;
+               virtual string getCitation() = 0;
+               virtual string getDescription() = 0;
+               
+               virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
+               virtual vector<string> setParameters() = 0; //to fill parameters
+               virtual vector<CommandParameter> getParameters() { return parameters; }
+       
                virtual int execute() = 0;
                virtual void help() = 0;
+               void citation() { m->mothurOutEndLine(); m->mothurOut(getCitation()); m->mothurOutEndLine(); }
                virtual ~Command() { }
+       
+       protected:
+               MothurOut* m;
+               bool calledHelp;
+                       
+               map<string, vector<string> > outputTypes;
+               vector<CommandParameter> parameters;
+       
+               map<string, vector<string> >::iterator itTypes;
 };
 
 #endif