added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / command.hpp

diff --git a/command.hpp b/command.hpp
index e418de83e772dd824d83a6989ba51e1a92b60e06..f5e09042234f1c39ac8010f859e6f69708871dc3 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -1,6 +1,6 @@
 #ifndef COMMAND_HPP
 #define COMMAND_HPP
-
+//test2
 /*
  *  command.h
  *  
@@ -10,15 +10,46 @@
  *
  */
 
-/*This class is a parent to all the command classes.  It has one pure int execute(). */
+/*This class is a parent to all the command classes.  */
 
-using namespace std;
 
 #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 string getOutputFileNameTag(string, string) = 0;  //we may not know the complete filename, because some commands use info from the file to create the output file name (ie label). but we do the ending tag which should be enough to find the output file name from a list. Allows for optional passing of the inputFileName for the commands that require its extension.
+               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