added pipeline commands which involved change to command factory and command class...

[mothur.git] / makegroupcommand.h

diff --git a/makegroupcommand.h b/makegroupcommand.h
index 23d4598122bd99bdbc0a5869b590034159361ba1..260deaa5637a580c24d6be89b1c8b822ba262591 100644 (file)
--- a/makegroupcommand.h
+++ b/makegroupcommand.h
@@ -15,8 +15,13 @@
 class MakeGroupCommand : public Command {
        
 public:
-       MakeGroupCommand(string);       
+       MakeGroupCommand(string);
+       MakeGroupCommand();     
        ~MakeGroupCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute(); 
        void help();    
        
@@ -24,7 +29,8 @@ private:
                
        string fastaFileName, groups, outputDir, filename;
        vector<string> fastaFileNames;
-       vector<string> groupsNames;
+       vector<string> groupsNames, outputNames;
+       map<string, vector<string> > outputTypes;
        
        bool abort;
 };