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

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 1c8fbc4da656bf5c4240c1be8cb4a7843b3ac72c..3240860fc329bed3b9551359a6ff1b23a16b8019 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -20,8 +20,13 @@ class GlobalData;
 class LibShuffCommand : public Command {
        
 public:
-       LibShuffCommand(string);        
+       LibShuffCommand(string);
+       LibShuffCommand();      
        ~LibShuffCommand(){};
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
 
@@ -45,6 +50,7 @@ private:
        bool abort;
        string outputFile, groups, userform, savegroups, outputDir;
        vector<string> Groups, outputNames; //holds groups to be used
+       map<string, vector<string> > outputTypes;
 };
 
 #endif