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

[mothur.git] / getsabundcommand.h

diff --git a/getsabundcommand.h b/getsabundcommand.h
index e2ea5d292fdf7bbd4e9a1d1fb58ab62a80549c6c..b5363e1bce548af4af74408593d855cac4da973c 100644 (file)
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -21,7 +21,12 @@ class GlobalData;
 class GetSAbundCommand : public Command {
 public:
        GetSAbundCommand(string);
+       GetSAbundCommand();
        ~GetSAbundCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -33,6 +38,8 @@ private:
        OrderVector* order;
        InputData* input;
        SAbundVector* sabund;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used